Pufa polyketide synthase systems and uses thereof

ABSTRACT

Disclosed are the complete polyunsaturated fatty acid (PUFA) polyketide synthase (PKS) systems from the bacterial microorganisms  Shewanella japonica  and  Shewanella olleyana , and biologically active fragments and homologues thereof. More particularly, this invention relates to nucleic acids encoding such PUFA PKS systems, to proteins and domains thereof that comprise such PUFA PKS systems, to genetically modified organisms (plants and microorganisms) comprising such PUFA PKS systems, and to methods of making and using the PUFA PKS systems disclosed herein. This invention also relates to genetically modified plants and microorganisms and methods to efficiently produce lipids enriched in various polyunsaturated fatty acids (PUFAs) as well as other bioactive molecules by manipulation of a PUFA polyketide synthase (PKS) system.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.11/689,453, filed Mar. 21, 2007, which is a continuation of U.S. patentapplication Ser. No. 10/965,017, filed Oct. 13, 2004, now U.S. Pat. No.7,217,856, which is a continuation-in-part of U.S. patent applicationSer. No. 10/810,352, filed Mar. 24, 2004, now U.S. Pat. No. 7,211,418,which claims priority under 35 U.S.C. § 119(e) from U.S. ProvisionalApplication Ser. No. 60/457,979, filed Mar. 26, 2003. U.S. applicationSer. No. 10/810,352, supra, is also a continuation-in-part of U.S.patent application Ser. No. 10/124,800, filed Apr. 16, 2002, whichclaims the benefit of priority under 35 U.S.C. § 119(e) to: U.S.Provisional Application Ser. No. 60/284,066, filed Apr. 16, 2001; U.S.Provisional Application Ser. No. 60/298,796, filed Jun. 15, 2001; andU.S. Provisional Application Ser. No. 60/323,269, filed Sep. 18, 2001.U.S. patent application Ser. No. 10/124,800, supra, is also acontinuation-in-part of U.S. application Ser. No. 09/231,899, filed Jan.14, 1999, now U.S. Pat. No. 6,566,583. Each of the above-identifiedpatent applications is incorporated herein by reference in its entiretyfor all purposes.

This application does not claim the benefit of priority from U.S.application Ser. No. 09/090,793, filed Jun. 4, 1998, now U.S. Pat. No.6,140,486, although U.S. application Ser. No. 09/090,793 is incorporatedherein by reference in its entirety.

FIELD OF THE INVENTION

This invention relates to polyunsaturated fatty acid (PUFA) polyketidesynthase (PKS) systems from bacterial microorganisms. More particularly,this invention relates to nucleic acids encoding PUFA PKS systems, toproteins and domains thereof that comprise PUFA PKS systems, togenetically modified organisms comprising such PUFA PKS systems, and tomethods of making and using the PUFA PKS systems disclosed herein. Thisinvention also relates to genetically modified plants and microorganismsand methods to efficiently produce lipids enriched in variouspolyunsaturated fatty acids (PUFAs) by manipulation of a PUFA polyketidesynthase (PKS) system.

BACKGROUND OF THE INVENTION

Polyketide synthase (PKS) systems are generally known in the art asenzyme complexes related to fatty acid synthase (FAS) systems, but whichare often highly modified to produce specialized products that typicallyshow little resemblance to fatty acids. It has now been shown, however,that polyketide synthase systems exist in marine bacteria and certainmicroalgae that are capable of synthesizing polyunsaturated fatty acids(PUFAs) from acetyl-CoA and malonyl-CoA. The PKS pathways for PUFAsynthesis in Shewanella and another marine bacteria, Vibrio marinus, aredescribed in detail in U.S. Pat. No. 6,140,486. The PKS pathways forPUFA synthesis in the eukaryotic Thraustochytrid, Schizochytrium isdescribed in detail in U.S. Pat. No. 6,566,583. The PKS pathways forPUFA synthesis in eukaryotes such as members of Thraustochytriales,including the complete structural description of the PUFA PKS pathway inSchizochytrium and the identification of the PUFA PKS pathway inThraustochytrium, including details regarding uses of these pathways,are described in detail in U.S. Patent Application Publication No.20020194641, published Dec. 19, 2002 (corresponding to U.S. patentapplication Ser. No. 10/124,800, filed Apr. 16, 2002). U.S. patentapplication Ser. No. 10/810,352, filed Mar. 24, 2004, discloses thecomplete structural description of the PUFA PKS pathway inThraustochytrium, and further detail regarding the production ofeicosapentaenoic acid (C20:5, ω-3) (EPA) and other PUFAs using suchsystems.

Researchers have attempted to exploit polyketide synthase (PKS) systemsthat have been traditionally described in the literature as falling intoone of three basic types, typically referred to as: Type I (modular oriterative), Type II, and Type III. For purposes of clarity, it is notedthat the Type I modular PKS system has previously also been referred toas simply a “modular” PKS system, and the Type I iterative PKS systemhas previously also been referred to simply as a “Type I” PKS system.The Type II system is characterized by separable proteins, each of whichcarries out a distinct enzymatic reaction. The enzymes work in concertto produce the end product and each individual enzyme of the systemtypically participates several times in the production of the endproduct. This type of system operates in a manner analogous to the fattyacid synthase (FAS) systems found in plants and bacteria. Type Iiterative PKS systems are similar to the Type II system in that theenzymes are used in an iterative fashion to produce the end product. TheType I iterative differs from Type II in that enzymatic activities,instead of being associated with separable proteins, occur as domains oflarger proteins. This system is analogous to the Type I FAS systemsfound in animals and fungi.

In contrast to the Type II systems, in Type I modular PKS systems, eachenzyme domain is used only once in the production of the end product.The domains are found in very large proteins and the product of eachreaction is passed on to another domain in the PKS protein.Additionally, in the PKS systems described above, if a carbon-carbondouble bond is incorporated into the end product, it is usually in thetrans configuration.

Type III systems have been more recently discovered and belong to theplant chalcone synthase family of condensing enzymes. Type III PKSs aredistinct from type I and type II PKS systems and utilize free CoAsubstrates in iterative condensation reactions to usually produce aheterocyclic end product.

Polyunsaturated fatty acids (PUFAs) are critical components of membranelipids in most eukaryotes (Lauritzen et al., Prog. Lipid Res. 40 1(2001); McConn et al., Plant J. 15, 521 (1998)) and are precursors ofcertain hormones and signaling molecules (Heller et al., Drugs 55, 487(1998); Creelman et al., Annu. Rev. Plant Physiol. Plant Mol. Biol. 48,355 (1997)). Known pathways of PUFA synthesis involve the processing ofsaturated 16:0 or 18:0 fatty acids (the abbreviation X:Y indicates anacyl group containing X carbon atoms and Y double bonds (usually cis inPUFAs); double-bond positions of PUFAs are indicated relative to themethyl carbon of the fatty acid chain (e.g., ω3 or ω6) with systematicmethylene interruption of the double bonds) derived from fatty acidsynthase (FAS) by elongation and aerobic desaturation reactions(Sprecher, Curr. Opin. Clin. Nutr. Metab. Care 2, 135 (1999);Parker-Barnes et al., Proc. Natl. Acad. Sci. USA 97, 8284 (2000);Shanklin et al., Annu. Rev. Plant Physiol. Plant Nol. Biol. 49, 611(1998)). Starting from acetyl-CoA, the synthesis of docosahexaenoic acid(DHA) requires approximately 30 distinct enzyme activities and nearly 70reactions including the four repetitive steps of the fatty acidsynthesis cycle. Polyketide synthases (PKSs) carry out some of the samereactions as FAS (Hopwood et al., Annu. Rev. Genet. 24, 37 (1990);Bentley et al., Annu. Rev. Microbiol. 53, 411 (1999)) and use the samesmall protein (or domain), acyl carrier protein (ACP), as a covalentattachment site for the growing carbon chain. However, in these enzymesystems, the complete cycle of reduction, dehydration and reduction seenin FAS is often abbreviated so that a highly derivatized carbon chain isproduced, typically containing many keto- and hydroxy-groups as well ascarbon-carbon double bonds typically in the trans configuration. Thelinear products of PKSs are often cyclized to form complex biochemicalsthat include antibiotics and many other secondary products (Hopwood etal., (1990) supra; Bentley et al., (1999), supra; Keating et al., Curr.Opin. Chem. Biol. 3, 598 (1999)).

Very long chain PUFAs such as docosahexaenoic acid (DHA; 22:6ω3) andeicosapentaenoic acid (EPA; 20:5ω3) have been reported from severalspecies of marine bacteria, including Shewanella sp (Nichols et al.,Curr. Op. Biotechnol. 10, 240 (1999); Yazawa, Lipids 31, S (1996);DeLong et al., Appl. Environ. Microbiol. 51, 730 (1986)). Analysis of agenomic fragment (cloned as plasmid pEPA) from Shewanella sp. strainSCRC2738 led to the identification of five open reading frames (Orfs),totaling 20 Kb, that are necessary and sufficient for EPA production inE. coli (Yazawa, (1996), supra). Several of the predicted proteindomains were homologues of FAS enzymes, while other regions showed nohomology to proteins of known function. At least 11 regions within thefive Orfs were identifiable as putative enzyme domains (See Metz et al.,Science 293:290-293 (2001)). When compared with sequences in the genedatabases, seven of these were more strongly related to PKS proteinsthan to FAS proteins. Included in this group were domains putativelyencoding malonyl-CoA:ACP acyltransferase (MAT), β-ketoacyl-ACP synthase(KS), β-ketoacyl-ACP reductase (KR), acyltransferase (AT),phosphopantetheine transferase, chain length (or chain initiation)factor (CLF) and a highly unusual cluster of six ACP domains (i.e., thepresence of more than two clustered ACP domains had not previously beenreported in PKS or FAS sequences). It is likely that the PKS pathway forPUFA synthesis that has been identified in Shewanella is widespread inmarine bacteria. Genes with high homology to the Shewanella gene clusterhave been identified in Photobacterium profundum (Allen et al., Appli.Environ. Microbiol. 65:1710 (1999)) and in Moritella marina (Vibriomarinus) (see U.S. Pat. No. 6,140,486, ibid., and Tanaka et al.,Biotechnol. Lett. 21:939 (1999)).

Polyunsaturated fatty acids (PUFAs) are considered to be useful fornutritional, pharmaceutical, industrial, and other purposes. The currentsupply of PUFAs from natural sources and from chemical synthesis is notsufficient for commercial needs. A major current source for PUFAs isfrom marine fish; however, fish stocks are declining, and this may notbe a sustainable resource. Additionally, contamination, from both heavymetals and toxic organic molecules, is a serious issue with oil derivedfrom marine fish. Vegetable oils derived from oil seed crops arerelatively inexpensive and do not have the contamination issuesassociated with fish oils. However, the PUFAs found in commerciallydeveloped plant oils are typically limited to linoleic acid (eighteencarbons with 2 double bonds, in the delta 9 and 12 positions—18:2 delta9,12) and linolenic acid (18:3 delta 9,12,15). In the conventionalpathway for PUFA synthesis, medium chain-length saturated fatty acids(products of a fatty acid synthase (FAS) system) are modified by aseries of elongation and desaturation reactions. Because a number ofseparate desaturase and elongase enzymes are required for fatty acidsynthesis from linoleic and linolenic acids to produce the moresaturated and longer chain PUFAs, engineering plant host cells for theexpression of PUFAs such as EPA and docosahexaenoic acid (DHA) mayrequire expression of several separate enzymes to achieve synthesis.Additionally, for production of useable quantities of such PUFAs,additional engineering efforts may be required, for example, engineeringthe down regulation of enzymes that compete for substrate, engineeringof higher enzyme activities such as by mutagenesis or targeting ofenzymes to plastid organelles. Therefore it is of interest to obtaingenetic material involved in PUFA biosynthesis from species thatnaturally produce these fatty acids and to express the isolated materialalone or in combination in a heterologous system which can bemanipulated to allow production of commercial quantities of PUFAs.

The discovery of a PUFA PKS system in marine bacteria such as Shewanellaand Vibrio marinus (see U.S. Pat. No. 6,140,486, ibid.), discussedabove, provided a resource for new methods of commercial PUFAproduction. However, the marine bacteria containing PUFA PKS systemsthat have been identified to date have limitations which may ultimatelyrestrict their usefulness on a commercial level. In particular, althoughU.S. Pat. No. 6,140,486 discloses that these marine bacteria PUFA PKSsystems can be used to genetically modify plants, the marine bacterianaturally live and grow in cold marine environments and the enzymesystems of these bacteria do not function well above 22° C. and mayoptimally function at much lower temperatures. In contrast, many cropplants, which are attractive targets for genetic manipulation using thePUFA PKS system, have normal growth conditions at temperatures above 22°C. and ranging to higher than 40° C. Therefore, the PUFA PKS systemsfrom these marine bacteria are not predicted to be readily adaptable toplant expression under normal growth conditions.

With regard to the production of eicosapentaenoic acid (EPA) inparticular, researchers have tried to produce EPA with microbes bygrowing them in both photosynthetic and heterotrophic cultures. Theyhave also used both classical and directed genetic approaches inattempts to increase the productively of the organisms under cultureconditions. Other researchers have attempted to produce EPA in oil-seedcrop plants by introduction of genes encoding various desaturase andelongase enzymes.

Researchers have attempted to use cultures of red microalgae (Monodus),diatoms (e.g. Phaeodacylum), other microalgae and fungi (e.g.Mortierella cultivated at low temperatures). However, in all cases,productivity was low compared to existing commercial microbialproduction systems for other long chain PUFAs such as DHA. In manycases, the EPA occurred primarily in the phospholipids (PL) rather thanthe triacylglycerols (TAG) form. Since productivity of microalgae underheterotrophic growth conditions can be much higher than underphototrophic conditions, researchers have attempted, and achieved,trophic conversion by introduction of genes encoding specific sugartransporters. However, even with the newly acquired heterotrophiccapability, productivity in terms of oil remained relatively low.

As discussed above, several marine bacteria have been shown to producePUFAs (EPA as well as DHA). However, these bacteria do not producesignificant quantities of TAG, and the EPA is found primarily in the PLmembrane form. The levels of EPA produced by these particular bacteriaas well as their growth characteristics (discussed above) limit theirutility for commercial production of EPA.

There have been many efforts to produce EPA in oil-seed crop plants bymodification of the endogenously-produced fatty acids. Geneticmodification of these plants with various individual genes for fattyacid elongases and desaturases has produced leaves or seeds containingsignificant levels of EPA but also containing significant levels ofmixed shorter-chain and less unsaturated PUFAs (Qi et al., NatureBiotech. 22:739 (2004); PCT Publication No. WO 04/071467; Abbadi et al.,Plant Cell 16:1 (2004)). In contrast, the known EPA-producing PUFA PKSsystems as described herein yield a PUFA profile that is essentiallypure EPA.

Therefore, there is a need in the art for other PUFA PKS systems havinggreater flexibility for commercial use, and for a biological system thatefficiently produces quantities of lipids (e.g., PL and TAG) enriched indesired PUFAs, such as EPA, in a commercially useful production process.

SUMMARY OF THE INVENTION

One embodiment of the present invention generally relates to isolatednucleic acid molecules encoding PUFA PKS proteins and domains fromShewanella japonica or Shewanella olleyana, and biologically activehomologues and fragments thereof. In one aspect, the invention includesan isolated nucleic acid molecule comprising a nucleic acid sequenceselected from: (a) a nucleic acid sequence encoding an amino acidsequence selected from the group consisting of: SEQ ID NO:2, SEQ IDNO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:9,SEQ ID NO:10, SEQ ID NO:11, and SEQ ID NO:12; (b) a nucleic acidsequence encoding a fragment of any of the amino acid sequences of (a)having at least one biological activity selected from the groupconsisting of enoyl-ACP reductase (ER) activity; acyl carrier protein(ACP) activity; β-ketoacyl-ACP synthase (KS) activity; acyltransferase(AT) activity; β-ketoacyl-ACP reductase (KR) activity; FabA-likeβ-hydroxyacyl-ACP dehydrase (DH) activity; non-FabA-like dehydraseactivity; chain length factor (CLF) activity; malonyl-CoA:ACPacyltransferase (MAT) activity; and 4′-phosphopantetheinyl transferase(PPTase) activity; (c) a nucleic acid sequence encoding an amino acidsequence that is at least about 65% identical, and more preferably atleast about 75% identical, and more preferably at least about 85%identical, and more preferably at least about 95% identical, to SEQ IDNO:2 or SEQ ID NO:8 and has at least one biological activity selectedfrom the group consisting of: KS activity, MAT activity, KR activity,ACP activity, and non-FabA-like dehydrase activity; (d) a nucleic acidsequence encoding an amino acid sequence that is at least about 60%identical, and more preferably at least about 70% identical, and morepreferably at least about 80% identical, and more preferably at leastabout 90% identical, to SEQ ID NO:3 or SEQ ID NO:9 and has AT biologicalactivity; (e) a nucleic acid sequence encoding an amino acid sequencethat is at least about 70% identical and more preferably at least about80% identical, and more preferably at least about 90% identical, andmore preferably at least about 95% identical, to SEQ ID NO:4 or SEQ IDNO:10 and has at least one biological activity selected from the groupconsisting of KS activity, CLF activity and DH activity; (f) a nucleicacid sequence encoding an amino acid sequence that is at least about 60%identical, and more preferably at least about 70% identical, and morepreferably at least about 80% identical, and more preferably at leastabout 90% identical, to SEQ ID NO:6 or SEQ ID NO:12 and has PPTasebiological activity; (g) a nucleic acid sequence encoding an amino acidsequence that is at least about 85% identical, and more preferably atleast about 95% identical, and more preferably at least about 96%identical, and more preferably at least about 97% identical, to SEQ IDNO:11, or at least about 95% identical, and more preferably at leastabout 96% identical, and more preferably at least about 97% identical,and more preferably at least about 98% identical, to SEQ ID NO:5, andhas ER biological activity.

In one aspect, the fragment set forth in (b) above is selected from:

(a) a fragment of SEQ ID NO:2 from about position 29 to about position513 of SEQ ID NO:2, wherein the domain has KS biological activity;

(b) a fragment of SEQ ID NO:2 from about position 625 to about position943 of SEQ ID NO:2, wherein the domain has MAT biological activity;

(c) a fragment of SEQ ID NO:2 from about position 1264 to about position1889 of SEQ ID NO:2, and subdomains thereof, wherein the domain orsubdomain thereof has ACP biological activity;

(d) a fragment of SEQ ID NO:2 from about position 2264 to about position2398 of SEQ ID NO:2, wherein the domain has KR biological activity;

(e) a fragment of SEQ ID NO:2 comprising from about position 2504 toabout position 2516 of SEQ ID NO:2, wherein the fragment hasnon-FabA-like dehydrase biological activity;

(f) a fragment of SEQ ID NO:3 from about position 378 to about position684 of SEQ ID NO:3, wherein the domain has AT biological activity;

(g) a fragment of SEQ ID NO:4 from about position 5 to about position483 of SEQ ID NO:4, wherein the domain has KS biological activity;

(h) a fragment of SEQ ID NO:4 from about position 489 to about position771 of SEQ ID NO:4, wherein the domain has CLF biological activity;

(i) a fragment of SEQ ID NO:4 from about position 1428 to about position1570 of SEQ ID NO:4, wherein the domain has DH biological activity;

(j) a fragment of SEQ ID NO:4 from about position 1881 to about position2019 of SEQ ID NO:4, wherein the domain has DH biological activity;

(k) a fragment of SEQ ID NO:5 from about position 84 to about position497 of SEQ ID NO:5, wherein the domain has ER biological activity;

(l) a fragment of SEQ ID NO:6 from about position 40 to about position186 of SEQ ID NO:6, wherein the domain has PPTase biological activity;

(m) a fragment of SEQ ID NO:8 from about position 29 to about position513 of SEQ ID NO:8, wherein the domain has KS biological activity;

(n) a fragment of SEQ ID NO:8 from about position 625 to about position943 of SEQ ID NO:8, wherein the domain has MAT biological activity;

(o) a fragment of SEQ ID NO:8 from about position 1275 to about position1872 of SEQ ID NO:8, and subdomains thereof, wherein the domain orsubdomain thereof has ACP biological activity;

(p) a fragment of SEQ ID NO:8 from about position 2240 to about position2374 of SEQ ID NO:8, wherein the domain has KR biological activity;

(q) a fragment of SEQ ID NO:8 comprising from about position 2480-2492of SEQ ID NO:8, wherein the fragment has non-FabA-like dehydraseactivity;

(r) a fragment of SEQ ID NO:9 from about position 366 to about position703 of SEQ ID NO:9, wherein the domain has AT biological activity;

(s) a fragment of SEQ ID NO:10 from about position 10 to about position488 of SEQ ID NO:10, wherein the domain has KS biological activity;

(t) a fragment of SEQ ID NO:10 from about position 502 to about position750 of SEQ ID NO:10, wherein the domain has CLF biological activity;

(u) a fragment of SEQ ID NO:10 from about position 1431 to aboutposition 1573 of SEQ ID NO:10, wherein the domain has DH biologicalactivity;

(v) a fragment of SEQ ID NO:10 from about position 1882 to aboutposition 2020 of SEQ ID NO:10, wherein the domain has DH biologicalactivity;

(w) a fragment of SEQ ID NO:11 from about position 84 to about position497 of SEQ ID NO:11, wherein the domain has ER biological activity; and

(x) a fragment of SEQ ID NO:12 from about position 29 to about position177 of SEQ ID NO:12, wherein the domain has PPTase biological activity.

Also included in the present invention are nucleic acid moleculesconsisting essentially of a nucleic acid sequence that is fullycomplementary to any of the above-identified the nucleic acid molecules.One aspect of the invention further relates to a recombinant nucleicacid molecule comprising any of the above-identified nucleic acidmolecules, operatively linked to at least one expression controlsequence. Another aspect of the invention relates to a recombinant celltransfected with any of the such recombinant nucleic acid molecules.

Another embodiment of the invention relates to a genetically modifiedplant or a part of the plant, wherein the plant has been geneticallymodified to recombinantly express a PKS system comprising at least onebiologically active protein or domain thereof of a polyunsaturated fattyacid (PUFA) polyketide synthase (PKS) system, wherein the protein ordomain is encoded by any of the above-described nucleic acid molecules.In one aspect, the genetically modified plant or part of a plant, as aresult of the genetic modification, produces one or more polyunsaturatedfatty acids selected from the group consisting of: DHA (docosahexaenoicacid (C22:6, ω-3)), ARA (eicosatetraenoic acid or arachidonic acid(C20:4, n-6)), DPA (docosapentaenoic acid (C22:5, ω-6 or ω-3)), and/orEPA (eicosapentaenoic acid (C20:5, ω-3). In particularly preferredembodiment, the plant or part of a plant produces DHA, EPA, EPA and DHA,ARA and DHA, or ARA and EPA. Genetically modified plants can include,crop plants, and any dicotyledonous plant or monocotyledonous plant.Preferred plants include, but are not limited to, canola, soybean,rapeseed, linseed, corn, safflower, sunflower and tobacco.

Yet another embodiment of the invention relates to a geneticallymodified microorganism, wherein the microorganism has been geneticallymodified to recombinantly express any of the above-described isolatednucleic acid molecules. In one aspect, the microorganism, as a result ofthe genetic modification, produces a polyunsaturated fatty acid selectedfrom the group consisting of: DHA (docosahexaenoic acid (C22:6, ω-3)),ARA (eicosatetraenoic acid or arachidonic acid (C20:4, n-6)), DPA(docosapentaenoic acid (C22:5, ω-6 or ω-3)), and/or EPA(eicosapentaenoic acid (C20:5, ω-3). In a particularly preferredembodiment, the microorganism, as a result of the genetic modification,produces DHA, EPA, EPA and DHA, ARA and DHA or ARA and EPA. In oneaspect, the microorganism is a Thraustochytrid, including, but notlimited to, Schizochytrium and Thraustochytrium. In one aspect, themicroorganism is a bacterium.

In one aspect, the above-described genetically modified plant ormicroorganism is genetically modified to recombinantly express a nucleicacid molecule encoding at least one amino acid sequence selected from:(a) an amino acid sequence selected from the group consisting of: SEQ IDNO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:8,SEQ ID NO:9, SEQ ID NO:10, SEQ ID NO:11, and SEQ ID NO:12; and (b) afragment of any of the amino acid sequences of (a) having at least onebiological activity selected from the group consisting of enoyl-ACPreductase (ER) activity; acyl carrier protein (ACP) activity;β-ketoacyl-ACP synthase (KS) activity; acyltransferase (AT) activity;β-ketoacyl-ACP reductase (KR) activity; FabA-like β-hydroxyacyl-ACPdehydrase (DH) activity; non-FabA-like dehydrase activity; chain lengthfactor (CLF) activity; malonyl-CoA:ACP acyltransferase (MAT) activity;and 4′-phosphopantetheinyl transferase (PPTase) activity. In one aspect,the plant is genetically modified to recombinantly express a nucleicacid molecule encoding at least one amino acid sequence selected from:SEQ ID NO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, and/or SEQ ID NO:6.In another aspect, the plant or microorganism is genetically modified torecombinantly express at least one nucleic acid molecule encoding SEQ IDNO:2, SEQ ID NO:3, SEQ ID NO:4, SEQ ID NO:5, and SEQ ID NO:6. In yetanother aspect, the plant or microorganism is genetically modified torecombinantly express a nucleic acid molecule encoding at least oneamino acid sequence selected from: SEQ ID NO:8, SEQ ID NO:9, SEQ IDNO:10, SEQ ID NO:11, and/or SEQ ID NO:12. In yet another aspect, theplant or microorganism is genetically modified to recombinantly expressat least one nucleic acid molecule encoding SEQ ID NO:8, SEQ ID NO:9,SEQ ID NO:10, SEQ ID NO:11, and SEQ ID NO:12. In another aspect, theplant or microorganism is genetically modified to recombinantly expressat least one nucleic acid molecule encoding any of the fragmentspreviously described above.

In one aspect of the genetically modified plant or part of a plant ormicroorganism embodiments of the invention, the plant or microorganismis additionally genetically modified to express at least onebiologically active protein or domain of a polyunsaturated fatty acid(PUFA) polyketide synthase (PKS) system from a Thraustochytrid,including, but not limited to, Schizochytrium and Thraustochytrium. Inone aspect, such a protein or domain comprises an amino acid sequenceselected from: (a) SEQ ID NO:14, SEQ ID NO:16, and SEQ ID NO:18; and (b)a fragment of any of the amino acid sequences of (a) having at least onebiological activity selected from the group consisting of enoyl-ACPreductase (ER) activity; acyl carrier protein (ACP) activity;β-ketoacyl-ACP synthase (KS) activity; acyltransferase (AT) activity;β-ketoacyl-ACP reductase (KR) activity; FabA-like β-hydroxyacyl-ACPdehydrase (DH) activity; non-FabA-like dehydrase activity; chain lengthfactor (CLF) activity; malonyl-CoA:ACP acyltransferase (MAT) activity;and 4′-phosphopantetheinyl transferase (PPTase) activity. In anotheraspect, the protein or domain comprises an amino acid sequence selectedfrom: (a) SEQ ID NO:20, SEQ ID NO:22, and SEQ ID NO:24; and (b) afragment of any of the amino acid sequences of (a) having at least onebiological activity selected from the group consisting of enoyl-ACPreductase (ER) activity; acyl carrier protein (ACP) activity;β-ketoacyl-ACP synthase (KS) activity; acyltransferase (AT) activity;β-ketoacyl-ACP reductase (KR) activity; FabA-like β-hydroxyacyl-ACPdehydrase (DH) activity; non-FabA-like dehydrase activity; chain lengthfactor (CLF) activity; malonyl-CoA:ACP acyltransferase (MAT) activity;and 4′-phosphopantetheinyl transferase (PPTase) activity.

In one aspect of the embodiment of the invention related to thegenetically modified microorganism, the microorganism comprises anendogenous PUFA PKS system. In this aspect, the endogenous PUFA PKSsystem can be modified by substitution of another isolated nucleic acidmolecule encoding at least one domain of a different PKS system for anucleic acid sequence encoding at least one domain of the endogenousPUFA PKS system. A different PKS system includes, but is not limited to,a non-bacterial PUFA PKS system, a bacterial PUFA PKS system, a type Imodular PKS system, a type I iterative PKS system, a type II PKS system,and a type III PKS system. In another aspect, the endogenous PUFA PKSsystem has been genetically modified by substitution of any of theabove-described isolated nucleic acid molecules of the invention for anucleic acid sequence encoding at least one domain of the endogenousPUFA PKS system. In another aspect, the microorganism has beengenetically modified to recombinantly express a nucleic acid moleculeencoding a chain length factor, or a chain length factor plus aβ-ketoacyl-ACP synthase (KS) domain, that directs the synthesis of C20units. In another aspect, the endogenous PUFA PKS system has beenmodified in a domain or domains selected from the group consisting of adomain encoding FabA-like β-hydroxy acyl-ACP dehydrase (DH) domain and adomain encoding β-ketoacyl-ACP synthase (KS), wherein the modificationalters the ratio of long chain fatty acids produced by the PUFA PKSsystem as compared to in the absence of the modification. Such amodification can include substituting a DH domain that does not possessisomerization activity for a FabA-like β-hydroxy acyl-ACP dehydrase (DH)in the endogenous PUFA PKS system. Such a modification can also includea deletion of all or a part of the domain, a substitution of ahomologous domain from a different organism for the domain, and amutation of the domain. In one aspect, the endogenous PUFA PKS systemhas been modified in an enoyl-ACP reductase (ER) domain, wherein themodification results in the production of a different compound ascompared to in the absence of the modification. In this aspect, such amodification can include a deletion of all or a part of the ER domain, asubstitution of an ER domain from a different organism for the ERdomain, and a mutation of the ER domain.

Another embodiment of the present invention relates to a method toproduce a bioactive molecule that is produced by a polyketide synthasesystem, comprising growing under conditions effective to produce thebioactive molecule, a genetically modified plant as described above.

Another embodiment of the present invention relates to a method toproduce a bioactive molecule that is produced by a polyketide synthasesystem, comprising culturing under conditions effective to produce thebioactive molecule, a genetically modified microorganism as describedabove.

In either of the two embodiments directly above, in one aspect, thegenetic modification changes at least one product produced by theendogenous PKS system, as compared to a wild-type organism. In anotheraspect, the organism produces a polyunsaturated fatty acid (PUFA)profile that differs from the naturally occurring organism without agenetic modification. In one aspect, the bioactive molecule is selectedfrom: an anti-inflammatory formulation, a chemotherapeutic agent, anactive excipient, an osteoporosis drug, an anti-depressant, ananti-convulsant, an anti-Heliobactor pylori drug, a drug for treatmentof neurodegenerative disease, a drug for treatment of degenerative liverdisease, an antibiotic, and a cholesterol lowering formulation. Inanother aspect, the bioactive molecule is an antibiotic. In anotheraspect, the bioactive molecule is a polyunsaturated fatty acid (PUFA).In yet another aspect, the bioactive molecule is a molecule includingcarbon-carbon double bonds in the cis configuration. In another aspect,the bioactive molecule is a molecule including a double bond at everythird carbon.

Another embodiment of the present invention relates to a method toproduce a plant that has a polyunsaturated fatty acid (PUFA) profilethat differs from the naturally occurring plant, comprising geneticallymodifying cells of the plant to express a PKS system comprising at leastone recombinant nucleic acid molecule of the present invention describedabove.

Another embodiment of the present invention relates to a method toproduce a recombinant microbe, comprising genetically modifyingmicrobial cells to express at least one recombinant nucleic acidmolecule of the present invention described above.

Yet another embodiment of the present invention relates to a method tomodify an endproduct to contain at least one fatty acid, comprisingadding to the endproduct an oil produced by a recombinant host cell thatexpresses at least one recombinant nucleic acid molecule of the presentinvention as described above. For example, the endproduct can include,but is not limited to, a dietary supplement, a food product, apharmaceutical formulation, a humanized animal milk, and an infantformula.

Yet another embodiment of the present invention relates to a method toproduce a humanized animal milk, comprising genetically modifyingmilk-producing cells of a milk-producing animal with at least onerecombinant nucleic acid molecule of the present invention as describedabove.

Another embodiment of the present invention relates to a recombinanthost cell which has been modified to express a recombinant bacterialpolyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system,wherein the PUFA PKS catalyzes both iterative and non-iterativeenzymatic reactions, and wherein the PUFA PKS system comprises: (a) atleast one enoyl ACP-reductase (ER) domain; (b) at least six acyl carrierprotein (ACP) domains; (c) at least two β-keto acyl-ACP synthase (KS)domains; (d) at least one acyltransferase (AT) domain; (e) at least oneketoreductase (KR) domain; (f) at least two FabA-like β-hydroxy acyl-ACPdehydrase (DH) domains; (g) at least one chain length factor (CLF)domain; (h) at least one malonyl-CoA:ACP acyltransferase (MAT) domain;and (i) at least one 4′-phosphopantetheinyl transferase (PPTase) domain.The PUFA PKS system produces PUFAs at temperatures of at least about 25°C. In one aspect, the PUFA PKS system comprises: (a) one enoylACP-reductase (ER) domain; (b) six acyl carrier protein (ACP) domains;(c) two β-keto acyl-ACP synthase (KS) domains; (d) one acyltransferase(AT) domain; (e) one ketoreductase (KR) domain; (f) two FabA-likeβ-hydroxy acyl-ACP dehydrase (DH) domains; (g) one chain length factor(CLF) domain; (h) one malonyl-CoA:ACP acyltransferase (MAT) domain; and(i) one 4′-phosphopantetheinyl transferase (PPTase) domain. In oneaspect, the PUFA PKS system is a PUFA PKS system from a marine bacteriumselected from the group consisting of Shewanella japonica and Shewanellaolleyana.

Yet another embodiment of the present invention relates to a geneticallymodified organism comprising at least one protein or domain of abacterial polyunsaturated fatty acid (PUFA) polyketide synthase (PKS)system, wherein the bacterial PUFA PKS system catalyzes both iterativeand non-iterative enzymatic reactions, wherein the bacterial PUFA PKSsystem produces PUFAs at temperatures of at least about 25° C., andwherein the bacterial PUFA PKS system comprises: (a) at least one enoylACP-reductase (ER) domain; (b) at least six acyl carrier protein (ACP)domains; (c) at least two β-keto acyl-ACP synthase (KS) domains; (d) atleast one acyltransferase (AT) domain; (e) at least one ketoreductase(KR) domain; (f) at least two FabA-like β-hydroxy acyl-ACP dehydrase(DH) domains; (g) at least one chain length factor (CLF) domain; (h) atleast one malonyl-CoA:ACP acyltransferase (MAT) domain; and (i) at leastone 4′-phosphopantetheinyl transferase (PPTase) domain. The geneticmodification affects the activity of the PUFA PKS system. In one aspect,the organism is modified to recombinantly express at least one proteinor domain of the bacterial PUFA PKS system. In another aspect, theorganism is modified to recombinantly express the bacterial PUFA PKSsystem. The organism can include a plant or a microorganism. In oneaspect, the bacterial PUFA PKS system is a PUFA PKS system from a marinebacterium selected from the group consisting of Shewanella japonica andShewanella olleyana. In another aspect, the organism expresses at leastone additional protein or domain from a second, different PKS system.

Another embodiment of the present invention relates to an isolatedrecombinant nucleic acid molecule encoding at least one protein orfunctional domain of a bacterial (PUFA) polyketide synthase (PKS)system, wherein the bacterial PUFA PKS system catalyzes both iterativeand non-iterative enzymatic reactions, wherein the bacterial PUFA PKSsystem produces PUFAs at temperatures of at least about 25° C., andwherein the bacterial PUFA PKS system comprises: (a) at least one enoylACP-reductase (ER) domain; (b) at least six acyl carrier protein (ACP)domains; (c) at least two β-keto acyl-ACP synthase (KS) domains; (d) atleast one acyltransferase (AT) domain; (e) at least one ketoreductase(KR) domain; (f) at least two FabA-like β-hydroxy acyl-ACP dehydrase(DH) domains; (g) at least one chain length factor (CLF) domain; (h) atleast one malonyl-CoA:ACP acyltransferase (MAT) domain; and (i) at leastone 4′-phosphopantetheinyl transferase (PPTase) domain.

BRIEF DESCRIPTION OF THE FIGURES OF THE INVENTION

FIG. 1 is a schematic drawing illustrating the open reading frame (ORF)architecture of EPA production clusters from Shewanella sp. SCRC-2738,Shewanella japonica, and Shewanella olleyana.

FIG. 2 is a schematic drawing illustrating the domain architecture ofthe EPA production gene clusters from Shewanella sp. SCRC-2738,Shewanella japonica and Shewanella olleyana.

FIG. 3A is a sequence alignment showing the overlap between the end ofpfaB ORF and the start of pfaC ORF (nucleotides 21101-21150 of SEQ IDNO:1, including the complementary strand, is shown) and theircorresponding amino acid translation (pfaB: positions 751-759 of SEQ IDNO:3; pfaC: positions 1-9 of SEQ ID NO:4) from Shewanella japonica(cosmid 3F3).

FIG. 3B is a sequence alignment showing the overlap between the end ofpfaB ORF and the start of pfaC ORF (nucleotides 27943-28008 of SEQ IDNO:7, including the complementary strand, is shown) and theircorresponding amino acid translation (pfaB: positions 735-742 of SEQ IDNO:9; pfaC: positions 1-9 of SEQ ID NO:10) from Shewanella olleyana(cosmid 9A10).

FIG. 4 is a sequence alignment showing the N-terminal end of the pfaEORFs (Sja_pfaE: positions 1-70 of SEQ ID NO:6; Sol_pfaE: positions 1-59of SEQ ID NO:12) versus the annotated start of orf2 from Shewanella sp.SCRC-2738 (orf2_ATG: SEQ ID NO:61) and the experimentally functionalstart of orf2 from Shewanella sp. SCRC-2738 (WO 98/55625) (orf2_TTG: SEQID NO:62).

DETAILED DESCRIPTION OF THE INVENTION

The present invention generally relates to polyunsaturated fatty acid(PUFA) polyketide synthase (PKS) systems from a subset of marinebacteria that naturally produce EPA and grow well at temperatures up toabout 30° C. and possibly higher (e.g., up to 35° C. or beyond), togenetically modified organisms comprising such PUFA PKS systems, tomethods of making and using such systems for the production of productsof interest, including bioactive molecules and particularly, PUFAs, suchas DHA, DPA and EPA.

As used herein, a PUFA PKS system (which may also be referred to as aPUFA synthase system) generally has the following identifying features:(1) it produces PUFAs as a natural product of the system; and (2) itcomprises several multifunctional proteins assembled into a complex thatconducts both iterative processing of the fatty acid chain as wellnon-iterative processing, including trans-cis isomerization and enoylreduction reactions in selected cycles. Reference to a PUFA PKS systemrefers collectively to all of the genes and their encoded products thatwork in a complex to produce PUFAs in an organism. Therefore, the PUFAPKS system refers specifically to a PKS system for which the naturalproducts are PUFAs.

More specifically, first, a PUFA PKS system that forms the basis of thisinvention produces polyunsaturated fatty acids (PUFAs) as products(i.e., an organism that endogenously (naturally) contains such a PKSsystem makes PUFAs using this system). The PUFAs referred to herein arepreferably polyunsaturated fatty acids with a carbon chain length of atleast 16 carbons, and more preferably at least 18 carbons, and morepreferably at least 20 carbons, and more preferably 22 or more carbons,with at least 3 or more double bonds, and preferably 4 or more, and morepreferably 5 or more, and even more preferably 6 or more double bonds,wherein all double bonds are in the cis configuration. It is an objectof the present invention to find or create via genetic manipulation ormanipulation of the endproduct, PKS systems which producepolyunsaturated fatty acids of desired chain length and with desirednumbers of double bonds. Examples of PUFAs include, but are not limitedto, DHA (docosahexaenoic acid (C22:6, ω-3)), ARA (eicosatetraenoic acidor arachidonic acid (C20:4, n-6)), DPA (docosapentaenoic acid (C22:5,ω-6 or ω-3)), and EPA (eicosapentaenoic acid (C20:5, ω-3)).

Second, the PUFA PKS system described herein incorporates both iterativeand non-iterative reactions, which generally distinguish the system frompreviously described PKS systems (e.g., type I modular or iterative,type II or type III). More particularly, the PUFA PKS system describedherein contains domains that appear to function during each cycle aswell as those which appear to function during only some of the cycles. Akey aspect of this functionality may be related to the domains showinghomology to the bacterial Fab-A enzymes. For example, the Fab-A enzymeof E. coli has been shown to possess two enzymatic activities. Itpossesses a dehydration activity in which a water molecule (H₂O) isabstracted from a carbon chain containing a hydroxy group, leaving atrans double bond in that carbon chain. In addition, it has an isomeraseactivity in which the trans double bond is converted to the cisconfiguration. This isomerization is accomplished in conjunction with amigration of the double bond position to adjacent carbons. In PKS (andFAS) systems, the main carbon chain is extended in 2 carbon increments.One can therefore predict the number of extension reactions required toproduce the PUFA products of these PKS systems. For example, to produceDHA (C22:6, all cis) requires 10 extension reactions. Since there areonly 6 double bonds in the end product, it means that during some of thereaction cycles, a double bond is retained (as a cis isomer), and inothers, the double bond is reduced prior to the next extension.

Before the discovery of a PUFA PKS system in marine bacteria (see U.S.Pat. No. 6,140,486), PKS systems were not known to possess thiscombination of iterative and selective enzymatic reactions, and theywere not thought of as being able to produce carbon-carbon double bondsin the cis configuration. However, the PUFA PKS system described by thepresent invention has the capacity to introduce cis double bonds and thecapacity to vary the reaction sequence in the cycle.

The present inventors propose to use these features of the PUFA PKSsystem to produce a range of bioactive molecules that could not beproduced by the previously described (Type I iterative or modular, TypeII, or Type III) PKS systems. These bioactive molecules include, but arenot limited to, polyunsaturated fatty acids (PUFAs), antibiotics orother bioactive compounds, many of which will be discussed below. Forexample, using the knowledge of the PUFA PKS gene structures describedherein, any of a number of methods can be used to alter the PUFA PKSgenes, or combine portions of these genes with other synthesis systems,including other PKS systems, such that new products are produced. Theinherent ability of this particular type of system to do both iterativeand selective reactions will enable this system to yield products thatwould not be found if similar methods were applied to other types of PKSsystems.

In U.S. patent application Ser. No. 10/810,352, supra, the presentinventors identified two exemplary marine bacteria (e.g. Shewanellaolleyana and Shewanella japonica) that are particularly suitable for useas sources of PUFA PKS genes, because they have the surprisingcharacteristic of being able to produce PUFAs (e.g., EPA) and grow attemperatures up to about 30° C., in contrast to previously describedPUFA PKS-containing marine bacteria, including other species and strainswithin Shewanella, which typically produce PUFAs and grow at much lowertemperatures. The inventors have now cloned and sequenced thefull-length genomic sequence of all of the PUFA PKS open reading frames(Orfs) in each of Shewanella olleyana (Australian Collection ofAntarctic Microorganisms (ACAM) strain number 644; Skerratt et al., Int.J. Syst. Evol. Microbiol 52, 2101 (2002)) and Shewanella japonica(American Type Culture Collection (ATCC) strain number BAA-316; Ivanovaet al., Int. J. Syst. Evol. Microbiol. 51, 1027 (2001)), and haveidentified the domains comprising the PUFA PKS system in these specialmarine bacteria. Therefore, the present invention solves theabove-mentioned problem of providing additional PUFA PKS systems thathave the flexibility for commercial use.

The PUFA PKS systems of the present invention can also be used as a toolin a strategy to solve the above-identified problem for production ofcommercially valuable lipids enriched in a desired PUFA, such as EPA, bythe present inventors' development of genetically modifiedmicroorganisms and methods for efficiently producing lipids enriched inPUFAs in one or more of their various forms (e.g., triacylglycerols(TAG) and phospholipids (PL)) by manipulation of the polyketidesynthase-like system that produces PUFAs in eukaryotes, includingmembers of the order Thraustochytriales such as Schizochytrium andThraustochytrium. Specifically, and by way of example, the presentinventors describe herein a strain of Schizochytrium that has previouslybeen optimized for commercial production of oils enriched in PUFA,primarily docosahexaenoic acid (DHA; C22:6 n-3) and docosapentaenoicacid (DPA; C22:5 n-6), and that will now be genetically modified suchthat EPA (C20:5 n-3) production (or other PUFA production) replaces theDHA production, without sacrificing the oil productivity characteristicsof the organism. One can use the marine bacterial PUFA PKS genes fromthe marine bacteria described in the present invention in one embodimentto produce such a genetically modified microorganism. This is only oneexample of the technology encompassed by the invention, as the conceptsof the invention can readily be applied to other production organismsand other desired PUFAs as described in detail below.

As used herein, the term “lipid” includes phospholipids; free fattyacids; esters of fatty acids; triacylglycerols; diacylglycerides;phosphatides; sterols and sterol esters; carotenoids; xanthophylls(e.g., oxycarotenoids); hydrocarbons; and other lipids known to one ofordinary skill in the art. The terms “polyunsaturated fatty acid” and“PUFA” include not only the free fatty acid form, but other forms aswell, such as the TAG form and the PL form.

In one embodiment, a PUFA PKS system according to the present inventioncomprises at least the following biologically active domains: (a) atleast one enoyl-ACP reductase (ER) domain; (b) at least six acyl carrierprotein (ACP) domains; (c) at least two β-ketoacyl-ACP synthase (KS)domains; (d) at least one acyltransferase (AT) domain; (e) at least oneβ-ketoacyl-ACP reductase (KR) domain; (f) at least two FabA-likeβ-hydroxyacyl-ACP dehydrase (DH) domains; (g) at least one chain lengthfactor (CLF) domain; and (h) at least one malonyl-CoA:ACPacyltransferase (MAT) domain. A PUFA PKS system also comprises at leastone 4′-phosphopantetheinyl transferase (PPTase) domain, and such domaincan be considered to be a part of the PUFA PKS system or an accessorydomain or protein to the PUFA PKS system. In one embodiment a PUFA PKSsystem according to the present invention also comprises at least oneregion containing a dehydratase (DH) conserved active site motif. Thefunctions of these domains and motifs are generally individually knownin the art and will be described in detail below with regard to the PUFAPKS system of the present invention. The domains of the presentinvention may be found as a single protein (i.e., the domain and proteinare synonymous) or as one of two or more (multiple) domains in a singleprotein. The domain architecture of the PUFA PKS systems in theseShewanella species is described in more detail below and is illustratedin FIG. 2.

In another embodiment, the PUFA PKS system comprises at least thefollowing biologically active domains: (a) at least one enoyl-ACPreductase (ER) domain; (b) multiple acyl carrier protein (ACP) domain(s)(at least from one to four, and preferably at least five, and morepreferably at least six, and even more preferably seven, eight, nine, ormore than nine); (c) at least two β-ketoacyl-ACP synthase (KS) domains;(d) at least one acyltransferase (AT) domain; (e) at least oneβ-ketoacyl-ACP reductase (KR) domain; (f) at least two FabA-likeβ-hydroxyacyl-ACP dehydrase (DH) domains; (g) at least one chain lengthfactor (CLF) domain; (h) at least one malonyl-CoA:ACP acyltransferase(MAT) domain; and (i) at least one 4′-phosphopantetheinyl transferase(PPTase) domain. In one embodiment a PUFA PKS system according to thepresent invention also comprises at least one region containing adehydratase (DH) conserved active site motif.

According to the present invention, a domain or protein havingβ-ketoacyl-ACP synthase (KS) biological activity (function) ischaracterized as the enzyme that carries out the initial step of the FAS(and PKS) elongation reaction cycle. The term “β-ketoacyl-ACP synthase”can be used interchangeably with the terms “3-keto acyl-ACP synthase”,“β-keto acyl-ACP synthase”, and “keto-acyl ACP synthase”, and similarderivatives. The acyl group destined for elongation is linked to acysteine residue at the active site of the enzyme by a thioester bond.In the multi-step reaction, the acyl-enzyme undergoes condensation withmalonyl-ACP to form -ketoacyl-ACP, CO₂ and free enzyme. The KS plays akey role in the elongation cycle and in many systems has been shown topossess greater substrate specificity than other enzymes of the reactioncycle. For example, E. coli has three distinct KS enzymes—each with itsown particular role in the physiology of the organism (Magnuson et al.,Microbiol. Rev. 57, 522 (1993)). The two KS domains of the PUFA-PKSsystems described herein could have distinct roles in the PUFAbiosynthetic reaction sequence.

As a class of enzymes, KS's have been well characterized. The sequencesof many verified KS genes are known, the active site motifs have beenidentified and the crystal structures of several have been determined.Proteins (or domains of proteins) can be readily identified as belongingto the KS family of enzymes by homology to known KS sequences.

According to the present invention, a domain or protein havingmalonyl-CoA:ACP acyltransferase (MAT) biological activity (function) ischaracterized as one that transfers the malonyl moiety from malonyl-CoAto ACP. The term “malonyl-CoA:ACP acyltransferase” can be usedinterchangeably with “malonyl acyltransferase” and similar derivatives.In addition to the active site motif (GxSxG), these enzymes possess anextended motif (R and Q amino acids in key positions) that identifiesthem as MAT enzymes (in contrast to the AT domain, discussed below). Insome PKS systems (but not the PUFA PKS domain), MAT domains willpreferentially load methyl- or ethyl-malonate on to the ACP group (fromthe corresponding CoA ester), thereby introducing branches into thelinear carbon chain. MAT domains can be recognized by their homology toknown MAT sequences and by their extended motif structure.

According to the present invention, a domain or protein having acylcarrier protein (ACP) biological activity (function) is characterized asbeing a small polypeptide (typically, 80 to 100 amino acids long), thatfunctions as a carrier for growing fatty acyl chains via a thioesterlinkage to a covalently bound co-factor of the protein. Thesepolypeptides occur as separate units or as domains within largerproteins. ACPs are converted from inactive apo-forms to functionalholo-forms by transfer of the phosphopantetheinyl moiety of CoA to ahighly conserved serine residue of the ACP. Acyl groups are attached toACP by a thioester linkage at the free terminus of thephosphopantetheinyl moiety. ACPs can be identified by labeling withradioactive pantetheine and by sequence homology to known ACPs. Thepresence of variations of an active site motif (LGIDS*; e.g., see aminoacids 1296-1300 of SEQ ID NO:2) is also a signature of an ACP.

According to the present invention, a domain or protein havingβ-ketoacyl-ACP reductase (KR) activity is characterized as one thatcatalyzes the pyridine-nucleotide-dependent reduction of 3-ketoacylforms of ACP. The term “β-ketoacyl-ACP reductase” can be usedinterchangeably with the terms “ketoreductase”, “3-ketoacyl-ACPreductase”, “keto-acyl ACP reductase” and similar derivatives of theterm. It is the first reductive step in the de novo fatty acidbiosynthesis elongation cycle and a reaction often performed inpolyketide biosynthesis. Significant sequence similarity is observedwith one family of enoyl-ACP reductases (ER), the other reductase of FAS(but not the ER family present in the PUFA PKS system), and theshort-chain alcohol dehydrogenase family. Pfam analysis of this PUFA PKSregion may reveal the homology to the short-chain alcohol dehydrogenasefamily in the core region. Blast analysis of the same region may revealmatches in the core area to known KR enzymes as well as an extendedregion of homology to domains from the other characterized PUFA PKSsystems.

According to the present invention, a domain or protein is referred toas a chain length factor (CLF) based on the following rationale. The CLFwas originally described as characteristic of Type II (dissociatedenzymes) PKS systems and was hypothesized to play a role in determiningthe number of elongation cycles, and hence the chain length, of the endproduct. CLF amino acid sequences show homology to KS domains (and arethought to form heterodimers with a KS protein), but they lack theactive site cysteine. The role of CLF in PKS systems has beencontroversial. Evidence (C. Bisang et al., Nature 401, 502 (1999))suggests a role in priming the PKS systems (by providing the initialacyl group to be elongated). In this role, the CLF domain is thought todecarboxylate malonate (as malonyl-ACP), thus forming an acetate groupthat can be transferred to the KS active site. This acetate thereforeacts as the ‘priming’ molecule that can undergo the initial elongation(condensation) reaction. Homologues of the Type II CLF have beenidentified as ‘loading’ domains in some type I modular PKS systems.However, other recent evidence suggests a genuine role of the CLFdomains in determining chain length (Yi et al., J. Am. Chem. Soc.125:12708 (2003). A domain with the sequence features of the CLF isfound in all currently identified PUFA PKS systems and in each case isfound as part of a multidomain protein.

Reference to an “acyltransferase” or “AT” refers to a general class ofenzymes that can carry out a number of distinct acyl transfer reactions.The term “acyltransferase” can be used interchangeably with the term“acyl transferase”. The Schizochytrium domain shows good homology to adomain present in all of the other PUFA PKS systems currently examinedand very weak homology to some acyltransferases whose specific functionshave been identified (e.g. to malonyl-CoA:ACP acyltransferase, MAT). Inspite of the weak homology to MAT, the AT domain is not believed tofunction as a MAT because it does not possess an extended motifstructure characteristic of such enzymes (see MAT domain description,above). For the purposes of this disclosure, the functions of the ATdomain in a PUFA PKS system include, but are not limited to: transfer ofthe fatty acyl group from the OrfA ACP domain(s) to water (i.e. athioesterase—releasing the fatty acyl group as a free fatty acid),transfer of a fatty acyl group to an acceptor such as CoA, transfer ofthe acyl group among the various ACP domains, or transfer of the fattyacyl group to a lipophilic acceptor molecule (e.g. to lysophosphadicacid).

According to the present invention, a protein or domain having enoyl-ACPreductase (ER) biological activity reduces the trans-double bond(introduced by the DH activity) in the fatty acyl-ACP, resulting infully saturating those carbons. The ER domain in the PUFA-PKS showshomology to a newly characterized family of ER enzymes (Heath et al.,Nature 406, 145 (2000)). According to the present invention, the term“enoyl-ACP reductase” can be used interchangeably with “enoylreductase”, “enoyl ACP-reductase” and “enoyl acyl-ACP reductase”. Heathand Rock identified this new class of ER enzymes by cloning a gene ofinterest from Streptococcus pneumoniae, purifying a protein expressedfrom that gene, and showing that it had ER activity in an in vitroassay. The bacterial PUFA PKS systems described herein contain one ERdomain.

According to the present invention, a protein or domain having dehydraseor dehydratase (DH) activity catalyzes a dehydration reaction. As usedgenerally herein, reference to DH activity typically refers to FabA-likeβ-hydroxyacyl-ACP dehydrase (DH) biological activity. FabA-likeβ-hydroxyacyl-ACP dehydrase (DH) biological activity removes HOH from aβ-ketoacyl-ACP and initially produces a trans double bond in the carbonchain. The term “FabA-like β-hydroxyacyl-ACP dehydrase” can be usedinterchangeably with the terms “FabA-like β-hydroxy acyl-ACP dehydrase”,“β-hydroxyacyl-ACP dehydrase”, “dehydrase” and similar derivatives. TheDH domains of the PUFA PKS systems show homology to bacterial DH enzymesassociated with their FAS systems (rather than to the DH domains ofother PKS systems). A subset of bacterial DH's, the FabA-like DH's,possesses cis-trans isomerase activity (Heath et al., J. Biol. Chem.,271, 27795 (1996)). It is the homology to the FabA-like DH proteins thatindicate that one or all of the DH domains described herein isresponsible for insertion of the cis double bonds in the PUFA PKSproducts.

A protein of the invention may also have dehydratase activity that isnot characterized as FabA-like (e.g., the cis-trans activity describedabove is associated with FabA-like activity), generally referred toherein as non-FabA-like DH activity, or non-FabA-like β-hydroxyacyl-ACPdehydrase (DH) biological activity. More specifically, a conservedactive site motif (˜13 amino acids long: L*xxHxxxGxxxxP; amino acids2504-2516 of SEQ ID NO:2; *in the motif, L can also be I) is found indehydratase domains in PKS systems (Donadio S, Katz L. Gene. 1992 Feb.1; 111(1):51-60). This conserved motif, also referred to herein as adehydratase (DH) conserved active site motif or DH motif, is found in asimilar region of all known PUFA-PKS sequences described to date and inthe PUFA PKS sequences described herein (e.g., amino acids 2504-2516 ofSEQ ID NO:2, or amino acids 2480-2492 of SEQ ID NO:8), but it isbelieved that his motif has been previously undetected until the presentinvention. This conserved motif is within an uncharacterized region ofhigh homology in the PUFA-PKS sequence. The proposed biosynthesis ofPUFAs via the PUFA-PKS requires a non-FabA like dehydration, and thismotif may be responsible for the reaction.

According to the present invention, a domain or protein having4′-phosphopantetheinyl transferase (PPTase) biological activity(function) is characterized as the enzyme that transfers a4′-phosphopantetheinyl moiety from Coenzyme A to the acyl carrierprotein (ACP). This transfer to an invariant serine reside of the ACPactivates the inactive apo-form to the holo-form. In both polyketide andfatty acid synthesis, the phosphopantetheine group forms thioesters withthe growing acyl chains. The PPTases are a family of enzymes that havebeen well characterized in fatty acid synthesis, polyketide synthesis,and non-ribosomal peptide synthesis. The sequences of many PPTases areknown, and crystal structures have been determined (e.g., Reuter K,Mofid M R, Marahiel M A, Ficner R. “Crystal structure of the surfactinsynthetase-activating enzyme sfp: a prototype of the4′-phosphopantetheinyl transferase superfamily” EMBO J. 1999 Dec. 1;18(23):6823-31) as well as mutational analysis of amino acid residuesimportant for activity (Mofid M R, Finking R, Essen L O, Marahiel M A.“Structure-based mutational analysis of the 4′-phosphopantetheinyltransferases Sfp from Bacillus subtilis: carrier protein recognition andreaction mechanism” Biochemistry. 2004 Apr. 13; 43(14):4128-36). Theseinvariant and highly conserved amino acids in PPTases are containedwithin the pfaE ORFs from both Shewanella strains described herein.Additionally, the pfaE ORF homolog in Shewanella sp. SCRC-2738 orf2 hasbeen shown to be required for activity in the native strain (Yazawa K.“Production of eicosapentaenoic acid from marine bacteria”. Lipids. 1996March; 31 Suppl:S297-300.) and labeling experiments confirming itsPPTase activity (WO 98/55625).

The PUFA PKS systems of particular marine bacteria (e.g., Shewanellaolleyana and Shewanella japonica) that produce PUFAs and grow well attemperatures of up to about 25-30° C., and possibly higher (e.g., 35°C.), are the basis of the present invention, although the presentinvention does contemplate the use of domains from these bacterial PUFAPKS systems in conjunction with domains from other bacterial andnon-bacterial PUFA PKS systems that have been described, for example, inU.S. Pat. No. 6,140,486, U.S. Pat. No. 6,566,583, U.S. patentapplication Ser. No. 10/124,800, and U.S. patent application Ser. No.10/810,352. More particularly, the PUFA PKS systems of the presentinvention can be used with other PUFA PKS systems to produce hybridconstructs and genetically modified microorganisms and plants forimproved and or modified production of biological products by suchmicroorganisms and plants. For example, according to the presentinvention, genetically modified organisms can be produced whichincorporate non-bacterial PUFA PKS functional domains with bacterialPUFA PKS functional domains (preferably those of the present invention),as well as PKS functional domains or proteins from other PKS systems(type I, type II, type III) or FAS systems.

Reference herein to a “non-bacterial PUFA PKS” system is reference to aPUFA PKS system that has been isolated from an organism that is not abacterium, or is a homologue of, or derived from, a PUFA PKS system froman organism that is not a bacterium, such as a eukaryote or anarchaebacterium. Eukaryotes are separated from prokaryotes based on thedegree of differentiation of the cells, with eukaryotes having morehighly differentiated cells and prokaryotes having less differentiatedcells. In general, prokaryotes do not possess a nuclear membrane, do notexhibit mitosis during cell division, have only one chromosome, theircytoplasm contains 70S ribosomes, they do not possess any mitochondria,endoplasmic reticulum, chloroplasts, lysosomes or Golgi apparatus, theirflagella (if present) consists of a single fibril. In contrast,eukaryotes have a nuclear membrane, they do exhibit mitosis during celldivision, they have many chromosomes, their cytoplasm contains 80Sribosomes, they do possess mitochondria, endoplasmic reticulum,chloroplasts (in algae), lysosomes and Golgi apparatus, and theirflagella (if present) consists of many fibrils. In general, bacteria areprokaryotes, while algae, fungi, protist, protozoa and higher plants areeukaryotes.

Non-bacterial PUFA PKS systems include those that have been described inthe above identified patents and applications, and particularly includeany PUFA PKS system isolated or derived from any Thraustochytrid. InU.S. Pat. No. 6,566,583, several cDNA clones from Schizochytrium showinghomology to Shewanella sp. strain SCRC2738 PKS genes were sequenced, andvarious clones were assembled into nucleic acid sequences representingtwo partial open reading frames and one complete open reading frame.Further sequencing of cDNA and genomic clones by the present inventorsallowed the identification of the full-length genomic sequence of eachof OrfA, OrfB and OrfC in Schizochytrium and the complete identificationof the domains in Schizochytrium with homology to those in Shewanella.These genes are described in detail in U.S. patent application Ser. No.10/124,800, supra and are described in some detail below. Similarly,U.S. patent application Ser. No. 10/810,352 describes in detail thefull-length genomic sequence of the genes encoding the PUFA PKS systemin a Thraustochytrium (specifically, Thraustochytrium sp. 23B (ATCC20892)) as well as the domains comprising the PUFA PKS system inThraustochytrium.

According to the present invention, the phrase “open reading frame” isdenoted by the abbreviation “Orf”. It is noted that the protein encodedby an open reading frame can also be denoted in all upper case lettersas “ORF” and a nucleic acid sequence for an open reading frame can alsobe denoted in all lower case letters as “orf”, but for the sake ofconsistency, the spelling “Orf” is preferentially used herein todescribe either the nucleic acid sequence or the protein encodedthereby. It will be obvious from the context of the usage of the termwhether a protein or nucleic acid sequence is referenced.

FIG. 1 shows the architecture of the PUFA PKS (also referred to as “EPAproduction”) clusters from Shewanella sp. SCRC-2738 (“Yazawa” strain;Yazawa K. “Production of eicosapentaenoic acid from marine bacteria”Lipids. 1996 March; 31 Suppl:S297-300.) versus the gene clusters of thepresent invention from Shewanella japonica (cosmid 3F3) and Shewanellaolleyana (cosmid 9A10). FIG. 2 shows the domain architecture of the PUFAPKS gene clusters from Shewanella sp. SCRC-2738 (“Yazawa” strain) versesthat encoded by the gene clusters from Shewanella japonica (cosmid 3F3)and Shewanella olleyana (cosmid 9A10). The domain structure of each openreading frame is described below.

Shewanella japonica PUFA PKS

SEQ ID NO:1 is the nucleotide sequence for Shewanella japonica cosmid3F3 and is found to contain 15 ORFs as detailed in Table 1 (see Example2). The ORFs related to the PUFA PKS system in this microorganism arecharacterized as follows.

pfaA (nucleotides 10491-18854 of SEQ ID NO:1) encodes PFAS A (SEQ IDNO:2), a PUFA PKS protein harboring the following domains:β-ketoacyl-synthase (KS) (nucleotides 10575-12029 of SEQ ID NO:1, aminoacids 29-513 of SEQ ID NO:2); malonyl-CoA: ACP acyltransferase (MAT)(nucleotides 12366-13319 of SEQ ID NO:1, amino acids 625-943 of SEQ IDNO:2); six tandem acyl-carrier proteins (ACP) domains (nucleotides14280-16157 of SEQ ID NO:1, amino acids 1264-1889 of SEQ ID NO:2);β-ketoacyl-ACP reductase (KR) (nucleotides 17280-17684 of SEQ ID NO:1,amino acids 2264-2398 of SEQ ID NO:2); and a region of the PFAS Aprotein between amino acids 2399 and 2787 of SEQ ID NO:2 containing adehydratase (DH) conserved active site motif LxxHxxxGxxxxP (amino acids2504-2516 of SEQ ID NO:2), referred to herein as DH-motif region.

In PFAS A, a KS active site DXAC* is located at amino acids 226-229 ofSEQ ID NO:2 with the C* being the site of the acyl attachment. A MATactive site, GHS*XG, is located at amino acids 721-725 of SEQ ID NO:2,with the S* being the acyl binding site. ACP active sites of LGXDS* arelocated at the following positions: amino acids 1296-1300, amino acids1402-1406, amino acids 1513-1517, amino acids 1614-1618, amino acids1728-1732, and amino acids 1843-1847 in SEQ ID NO:2, with the S* beingthe phosphopantetheine attachment site. Between amino acids 2399 and2787 of SEQ ID NO:2, the PFAS A also contains the dehydratase (DH)conserved active site motif LxxHxxxGxxxxP (amino acids 2504-2516 of SEQID NO:2) referenced above.

pfaB (nucleotides 18851-21130 of SEQ ID NO:1) encodes PFAS B (SEQ IDNO:3), a PUFA PKS protein harboring the following domain:acyltransferase (AT) (nucleotides 19982-20902 of SEQ ID NO:1, aminoacids 378-684 of SEQ ID NO:3).

In PFAS B, an active site GXS*XG motif is located at amino acids 463-467of SEQ ID NO:3, with the S* being the site of acyl-attachment.

pfaC (nucleotides 21127-27186 of SEQ ID NO:1) encodes PFAS C (SEQ IDNO:4), a PUFA PKS protein harboring the following domains: KS(nucleotides 21139-22575 of SEQ ID NO:1, amino acids 5-483 of SEQ IDNO:4); chain length factor (CLF) (nucleotides 22591-23439 of SEQ IDNO:1, amino acids 489-771 of SEQ ID NO:4); and two FabA3-hydroxyacyl-ACP dehydratases, referred to as DH1 (nucleotides25408-25836 of SEQ ID NO:1, amino acids 1428-1570 of SEQ ID NO:4) andDH2 (nucleotides 26767-27183 of SEQ ID NO:1, amino acids 1881-2019 ofSEQ ID NO:4).

In PFAS C, a KS active site DXAC* is located at amino acids 211-214 ofSEQ ID NO:4 with the C* being the site of the acyl attachment.

pfaD (nucleotides 27197-28825 of SEQ ID NO:1) encodes the PFAS D (SEQ IDNO:5), a PUFA PKS protein harboring the following domain: an enoylreductase (ER) (nucleotides 27446-28687 of SEQ ID NO:1, amino acids84-497 of SEQ ID NO:5).

pfaE (nucleotides 6150-7061 of SEQ ID NO:1 on the reverse complementarystrand) encodes PFAS E (SEQ ID NO:6), a 4′-phosphopantetheinyltransferase (PPTase) with the identified domain (nucleotides 6504-6944of SEQ ID NO:1, amino acids 40-186 of SEQ ID NO:6).

Shewanella olleyana PUFA PKS

SEQ ID NO:7 is the nucleotide sequence for Shewanella olleyana cosmid9A10 and was found to contain 17 ORFs as detailed in Table 2 (seeExample 2). The ORFs related to the PUFA PKS system in thismicroorganism are characterized as follows.

pfaA (nucleotides 17437-25743 of SEQ ID NO:7) encodes PFAS A (SEQ IDNO:8), a PUFA PKS protein harboring the following domains:β-ketoacyl-synthase (KS) (nucleotides 17521-18975 of SEQ ID NO:7, aminoacids 29-513 of SEQ ID NO:8); malonyl-CoA: ACP acyltransferase (MAT)(nucleotides 19309-20265 of SEQ ID NO:7, amino acids 625-943 of SEQ IDNO:8); six tandem acyl-carrier proteins (ACP) domains (nucleotides21259-23052 of SEQ ID NO:7, amino acids 1275-1872 of SEQ ID NO:8);β-ketoacyl-ACP reductase (KR) (nucleotides 24154-24558 of SEQ ID NO:7,amino acids 2240-2374 of SEQ ID NO:8); and a region of the PFAS Aprotein between amino acids 2241 and 2768 of SEQ ID NO:8 containing adehydratase (DH) conserved active site motif LxxHxxxGxxxxP (amino acids2480-2492 of SEQ ID NO:8), referred to herein as DH-motif region.

In PFAS A, a KS active site DXAC* is located at AA 226-229 of SEQ IDNO:8 with the C* being the site of the acyl attachment. A MAT activesite, GHS*XG, is located at amino acids 721-725 of SEQ ID NO:8 with theS* being the acyl binding site. ACP active sites of LGXDS* are locatedat: amino acids 1307-1311, amino acids 1408-1412, amino acids 1509-1513,amino acids 1617-1621, amino acids 1721-1725, and amino acids 1826-1830in SEQ ID NO:8, with the S* being the phosphopantetheine attachmentsite. Between amino acids 2241 and 2768 of SEQ ID NO:8, the PFAS A alsocontains the dehydratase (DH) conserved active site motif LxxHxxxGxxxxP(amino acids 2480-2492 of SEQ ID NO:8) referenced above.

pfaB (nucleotides 25740-27971 of SEQ ID NO:7) encodes PFAS B (SEQ IDNO:9), a PUFA PKS protein harboring the following domain:acyltransferase (AT) (nucleotides 26837-27848 of SEQ ID NO:1, aminoacids 366-703 of SEQ ID NO:9).

In PFAS B, an active site GXS*XG motif is located at amino acids 451-455of SEQ ID NO:9 with the S* being the site of acyl-attachment.

pfaC (nucleotides 27968-34030 of SEQ ID NO:7) encodes PFAS C (SEQ IDNO:10), a PUFA PKS protein harboring the following domains: KS(nucleotides 27995-29431 SEQ ID NO:7, amino acids 10-488 SEQ ID NO:10);chain length factor (CLF) (nucleotides 29471-30217 SEQ ID NO:7, aminoacids 502-750 SEQ ID NO:10); and two FabA 3-hydroxyacyl-ACPdehydratases, referred to as DH1 (nucleotides 32258-32686 SEQ ID NO:7,amino acids 1431-1573 SEQ ID NO:10), and DH2 (nucleotides 33611-34027 ofSEQ ID NO:7, amino acids 1882-2020 of SEQ ID NO:10).

In PFAS C, a KS active site DXAC* is located at amino acids 216-219 ofSEQ ID NO:10 with the C* being the site of the acyl attachment.

pfaD (nucleotides 34041-35669 of SEQ ID NO:7) encodes the PFAS D (SEQ IDNO:11), a PUFA PKS protein harboring the following domain: an enoylreductase (ER) (nucleotides 34290-35531 of SEQ ID NO:7, amino acids84-497 of SEQ ID NO:11).

pfaE (nucleotides 13027-13899 of SEQ ID NO:7 on the reversecomplementary strand) encodes PFAS E (SEQ ID NO:12), a4′-phosphopantetheinyl transferase (PPTase) with the identified domain(nucleotides 13369-13815 of SEQ ID NO:7, amino acid 29-177 of SEQ IDNO:12).

The pfaC ORF from both Shewanella strains described above and the pfaEORF from Shewanella olleyana are predicted to have TTG as their startcodon. While TTG is a less common start codon in bacteria then ATG andGTG, it has been predicted to be the start codon for 1.1% of E. coligenes and 11.2% of Bacillus subtilis genes (Hannenhalli S S, Hayes W S,Hatzigeorgiou A G, Fickett J W. “Bacterial start site prediction”.Nucleic Acids Res. 1999 Sep. 1; 27(17):3577-82). There are several linesof evidence to annotate these ORFs start with a TTG codon. First, bothcomputational gene finding tools (EasyGene and GeneMark.hmm) predictedthe TTG start codon for these three ORFs. Second, translation from theTTG start in these three ORFs conserves the spacing and range ofidentical and similar protein residues to homologous genes in theGenBank database. Another line of evidence for the TTG start codon inthese genes is the predicted ribosome binding sites (RBS). The RBS isapproximately 7 to 12 nucleotides upstream of the start codon and isusually purine rich. Table 5 (see Example 2) shows the upstream regionsof all the pfa ORFs and possible RBS. Both pfaC ORFs show very highhomology to canonical RBS upstream of the TTG start codon. Alternativestarting codons and RBS for these three ORFs annotated with the TTGstart codon are also shown in Table 5. It is also noted that the pfaEORFs from the Shewanella strains described here are homologous to orf2from the EPA biosynthetic cluster from Shewanella sp. SCRC-2738 (GenBankaccession number U73935). Expression of the Shewanella sp. SCRC-2738orf2 from the annotated ATG was shown not to support EPA production in aheterologous expression system (see PCT Publication No. WO 98/55625).When an alternate upstream start codon of TTG was used in theexpression, EPA production was seen in a heterologous expression system.The annotated start codons for both pfaE ORFs described here encodesimilar and identical amino acids to those encoded from the alternateTTG start codon from orf2 of Shewanella sp. SCRC-2738 (FIG. 4). Thisalso supports the TTG start annotation for pfaE ORF from Sh. olleyana.Lastly, the pfaC ORF start codons from both Shewanella strains overlapwith the pfaB stop codons (FIG. 3). The overlap of ORFs is a commonfeature in bacterial operons and is thought to be one means for couplingtwo or more genes at the transcriptional level.

One embodiment of the present invention relates to an isolated proteinor domain from a bacterial PUFA PKS system described herein, a homologuethereof, and/or a fragment thereof. Also included in the invention areisolated nucleic acid molecules encoding any of the proteins, domains orpeptides described herein (discussed in detail below). According to thepresent invention, an isolated protein or peptide, such as a protein orpeptide from a PUFA PKS system, is a protein or a fragment thereof(including a polypeptide or peptide) that has been removed from itsnatural milieu (i.e., that has been subject to human manipulation) andcan include purified proteins, partially purified proteins,recombinantly produced proteins, and synthetically produced proteins,for example. As such, “isolated” does not reflect the extent to whichthe protein has been purified. Preferably, an isolated protein of thepresent invention is produced recombinantly. An isolated peptide can beproduced synthetically (e.g., chemically, such as by peptide synthesis)or recombinantly. In addition, and by way of example, a “Shewanellajaponica PUFA PKS protein” refers to a PUFA PKS protein (generallyincluding a homologue of a naturally occurring PUFA PKS protein) from aShewanella japonica microorganism, or to a PUFA PKS protein that hasbeen otherwise produced from the knowledge of the structure (e.g.,sequence), and perhaps the function, of a naturally occurring PUFA PKSprotein from Shewanella japonica. In other words, general reference to aShewanella japonica PUFA PKS protein includes any PUFA PKS protein thathas substantially similar structure and function of a naturallyoccurring PUFA PKS protein from Shewanella japonica or that is abiologically active (i.e., has biological activity) homologue of anaturally occurring PUFA PKS protein from Shewanella japonica asdescribed in detail herein. As such, a Shewanella japonica PUFA PKSprotein can include purified, partially purified, recombinant,mutated/modified and synthetic proteins. The same description applies toreference to other proteins or peptides described herein, such as thePUFA PKS proteins and domains from Shewanella olleyana.

According to the present invention, the terms “modification” and“mutation” can be used interchangeably, particularly with regard to themodifications/mutations to the primary amino acid sequences of a proteinor peptide (or nucleic acid sequences) described herein. The term“modification” can also be used to describe post-translationalmodifications to a protein or peptide including, but not limited to,methylation, farnesylation, carboxymethylation, geranyl geranylation,glycosylation, phosphorylation, acetylation, myristoylation,prenylation, palmitation, and/or amidation. Modifications can alsoinclude, for example, complexing a protein or peptide with anothercompound. Such modifications can be considered to be mutations, forexample, if the modification is different than the post-translationalmodification that occurs in the natural, wild-type protein or peptide.

As used herein, the term “homologue” is used to refer to a protein orpeptide which differs from a naturally occurring protein or peptide(i.e., the “prototype” or “wild-type” protein) by one or more minormodifications or mutations to the naturally occurring protein orpeptide, but which maintains the overall basic protein and side chainstructure of the naturally occurring form (i.e., such that the homologueis identifiable as being related to the wild-type protein). Such changesinclude, but are not limited to: changes in one or a few amino acid sidechains; changes one or a few amino acids, including deletions (e.g., atruncated version of the protein or peptide) insertions and/orsubstitutions; changes in stereochemistry of one or a few atoms; and/orminor derivatizations, including but not limited to: methylation,farnesylation, geranyl geranylation, glycosylation, carboxymethylation,phosphorylation, acetylation, myristoylation, prenylation, palmitation,and/or amidation. A homologue can have either enhanced, decreased, orsubstantially similar properties as compared to the naturally occurringprotein or peptide. Preferred homologues of a PUFA PKS protein or domainare described in detail below. It is noted that homologues can includesynthetically produced homologues, naturally occurring allelic variantsof a given protein or domain, or homologous sequences from organismsother than the organism from which the reference sequence was derived.

Conservative substitutions typically include substitutions within thefollowing groups: glycine and alanine; valine, isoleucine and leucine;aspartic acid, glutamic acid, asparagine, and glutamine; serine andthreonine; lysine and arginine; and phenylalanine and tyrosine.Substitutions may also be made on the basis of conserved hydrophobicityor hydrophilicity (Kyte and Doolittle, J. Mol. Biol. 157:105 (1982)), oron the basis of the ability to assume similar polypeptide secondarystructure (Chou and Fasman, Adv. Enzymol. 47: 45 (1978)).

Homologues can be the result of natural allelic variation or naturalmutation. A naturally occurring allelic variant of a nucleic acidencoding a protein is a gene that occurs at essentially the same locus(or loci) in the genome as the gene which encodes such protein, butwhich, due to natural variations caused by, for example, mutation orrecombination, has a similar but not identical sequence. Allelicvariants typically encode proteins having similar activity to that ofthe protein encoded by the gene to which they are being compared. Oneclass of allelic variants can encode the same protein but have differentnucleic acid sequences due to the degeneracy of the genetic code.Allelic variants can also comprise alterations in the 5′ or 3′untranslated regions of the gene (e.g., in regulatory control regions).Allelic variants are well known to those skilled in the art.

Homologues can be produced using techniques known in the art for theproduction of proteins including, but not limited to, directmodifications to the isolated, naturally occurring protein, directprotein synthesis, or modifications to the nucleic acid sequenceencoding the protein using, for example, classic or recombinant DNAtechniques to effect random or targeted mutagenesis.

Modifications or mutations in protein homologues, as compared to thewild-type protein, either increase, decrease, or do not substantiallychange, the basic biological activity of the homologue as compared tothe naturally occurring (wild-type) protein. In general, the biologicalactivity or biological action of a protein refers to any function(s)exhibited or performed by the protein that is ascribed to the naturallyoccurring form of the protein as measured or observed in vivo (i.e., inthe natural physiological environment of the protein) or in vitro (i.e.,under laboratory conditions). Biological activities of PUFA PKS systemsand the individual proteins/domains that make up a PUFA PKS system havebeen described in detail elsewhere herein. Modifications of a protein,such as in a homologue, may result in proteins having the samebiological activity as the naturally occurring protein, or in proteinshaving decreased or increased biological activity as compared to thenaturally occurring protein. Modifications which result in a decrease inprotein expression or a decrease in the activity of the protein, can bereferred to as inactivation (complete or partial), down-regulation, ordecreased action (or activity) of a protein. Similarly, modificationswhich result in an increase in protein expression or an increase in theactivity of the protein, can be referred to as amplification,overproduction, activation, enhancement, up-regulation or increasedaction (or activity) of a protein. It is noted that general reference toa homologue having the biological activity of the wild-type protein doesnot necessarily mean that the homologue has identical biologicalactivity as the wild-type protein, particularly with regard to the levelof biological activity. Rather, a homologue can perform the samebiological activity as the wild-type protein, but at a reduced orincreased level of activity as compared to the wild-type protein. Afunctional domain of a PUFA PKS system is a domain (i.e., a domain canbe a portion of a protein) that is capable of performing a biologicalfunction (i.e., has biological activity).

Methods of detecting and measuring PUFA PKS protein or domain biologicalactivity include, but are not limited to, measurement of transcriptionof a PUFA PKS protein or domain, measurement of translation of a PUFAPKS protein or domain, measurement of posttranslational modification ofa PUFA PKS protein or domain, measurement of enzymatic activity of aPUFA PKS protein or domain, and/or measurement production of one or moreproducts of a PUFA PKS system (e.g., PUFA production). It is noted thatan isolated protein of the present invention (including a homologue) isnot necessarily required to have the biological activity of thewild-type protein. For example, a PUFA PKS protein or domain can be atruncated, mutated or inactive protein, for example. Such proteins areuseful in screening assays, for example, or for other purposes such asantibody production. In a preferred embodiment, the isolated proteins ofthe present invention have a biological activity that is similar to thatof the wild-type protein (although not necessarily equivalent, asdiscussed above).

Methods to measure protein expression levels generally include, but arenot limited to: Western blot, immunoblot, enzyme-linked immunosorbantassay (ELISA), radioimmunoassay (RIA), immunoprecipitation, surfaceplasmon resonance, chemiluminescence, fluorescent polarization,phosphorescence, immunohistochemical analysis, matrix-assisted laserdesorption/ionization time-of-flight (MALDI-TOF) mass spectrometry,microcytometry, microarray, microscopy, fluorescence activated cellsorting (FACS), and flow cytometry, as well as assays based on aproperty of the protein including but not limited to enzymatic activityor interaction with other protein partners. Binding assays are also wellknown in the art. For example, a BIAcore machine can be used todetermine the binding constant of a complex between two proteins. Thedissociation constant for the complex can be determined by monitoringchanges in the refractive index with respect to time as buffer is passedover the chip (O'Shannessy et al. Anal. Biochem. 212:457 (1993);Schuster et al., Nature 365:343 (1993)). Other suitable assays formeasuring the binding of one protein to another include, for example,immunoassays such as enzyme linked immunoabsorbent assays (ELISA) andradioimmunoassays (RIA); or determination of binding by monitoring thechange in the spectroscopic or optical properties of the proteinsthrough fluorescence, UV absorption, circular dichroism, or nuclearmagnetic resonance (NMR).

In one embodiment, the present invention relates to an isolated proteincomprising, consisting essentially of, or consisting of, an amino acidsequence selected from: any one of SEQ ID NOs:2-6 or 8-12, orbiologically active domains or fragments thereof. The domains containedwithin the PUFA PKS proteins represented by SEQ ID NOs:2-6 and 8-12 havebeen described in detail above. In another embodiment, the presentinvention relates to an isolated homologue of a protein represented byany one of SEQ ID NOs:2-6 and 8-12. Such a homologue comprises, consistsessentially of, or consists of, an amino acid sequence that is at leastabout 60% identical to any one of SEQ ID NOs: 2-6 or 8-12 and has abiological activity of at least one domain that is contained within thecorresponding protein represented by SEQ ID NOs:2-6 or 8-12. In afurther embodiment, the present invention relates to a homologue of adomain of a PUFA PKS protein represented by any one of SEQ ID NO:2-6 or8-12, wherein the homologue comprises, consists essentially of, orconsists of, an amino acid sequence that is at least about 60% identicalto a domain from any one of SEQ ID NOs:2-6 or 8-12, and which has abiological activity of such domain from any one of SEQ ID NOs:2-6 or8-12. In additional embodiments, any of the above-described homologuesis at least about 65% identical, and more preferably at least about 70%identical, and more preferably at least about 75% identical, and morepreferably at least about 80% identical, and more preferably at leastabout 85% identical, and more preferably at least about 90% identical,and more preferably at least about 95% identical, and more preferably atleast about 96% identical, and more preferably at least about 97%identical, and more preferably at least about 98% identical, and morepreferably at least about 99% identical (or any percentage between 60%and 99%, in whole single percentage increments) to any one of SEQ IDNOs:2-6 or 8-12, or to a domain contained within these sequences. Asabove, the homologue preferably has a biological activity of the proteinor domain from which it is derived or related (i.e., the protein ordomain having the reference amino acid sequence).

One embodiment of the invention relates to an isolated homologue of aprotein represented by SEQ ID NO:2 that comprises, consists essentiallyof, or consists of, an amino acid sequence that is at least about 65%identical to SEQ ID NO:2 or to a biologically active domain within SEQID NO:2 as previously described herein, wherein the homologue has abiological activity of at least one domain that is contained within thecorresponding protein represented by SEQ ID NO:2. In additionalembodiments, the homologue is at least about 70% identical, and morepreferably at least about 75% identical, and more preferably at leastabout 80% identical, and more preferably at least about 85% identical,and more preferably at least about 90% identical, and more preferably atleast about 95% identical, and more preferably at least about 96%identical, and more preferably at least about 97% identical, and morepreferably at least about 98% identical, and more preferably at leastabout 99% identical (or any percentage between 65% and 99%, in wholesingle percentage increments) to SEQ ID NO:2 or a domain thereof.

Another embodiment of the invention relates to an isolated homologue ofa protein represented by SEQ ID NO:3 that comprises, consistsessentially of, or consists of, an amino acid sequence that is at leastabout 60% identical to SEQ ID NO:3 or to a biologically active domainwithin SEQ ID NO:3 as previously described herein, wherein the homologuehas a biological activity of at least one domain that is containedwithin the corresponding protein represented by SEQ ID NO:3. Inadditional embodiments, the homologue is at least about 65% identical,and more preferably at least about 70% identical, and more preferably atleast about 75% identical, and more preferably at least about 80%identical, and more preferably at least about 85% identical, and morepreferably at least about 90% identical, and more preferably at leastabout 95% identical, and more preferably at least about 96% identical,and more preferably at least about 97% identical, and more preferably atleast about 98% identical, and more preferably at least about 99%identical (or any percentage between 60% and 99%, in whole singlepercentage increments) to SEQ ID NO:3 or a domain thereof.

Another embodiment of the invention relates to an isolated homologue ofa protein represented by SEQ ID NO:4 that comprises, consistsessentially of, or consists of, an amino acid sequence that is at leastabout 70% identical to SEQ ID NO:4 or to a biologically active domainwithin SEQ ID NO:4 as previously described herein, wherein the homologuehas a biological activity of at least one domain that is containedwithin the corresponding protein represented by SEQ ID NO:4. Inadditional embodiments, the homologue is at least about 75% identical,and more preferably at least about 80% identical, and more preferably atleast about 85% identical, and more preferably at least about 90%identical, and more preferably at least about 95% identical, and morepreferably at least about 96% identical, and more preferably at leastabout 97% identical, and more preferably at least about 98% identical,and more preferably at least about 99% identical (or any percentagebetween 60% and 99%, in whole single percentage increments) to SEQ IDNO:4 or a domain thereof.

Another embodiment of the invention relates to an isolated homologue ofa protein represented by SEQ ID NO:5 that comprises, consistsessentially of, or consists of, an amino acid sequence that is at leastabout 95% identical to SEQ ID NO:5 or to a biologically active domainwithin SEQ ID NO:5 as previously described herein, wherein the homologuehas a biological activity of at least one domain that is containedwithin the corresponding protein represented by SEQ ID NO:5. Inadditional embodiments, the homologue is at least about 96% identical,and more preferably at least about 97% identical, and more preferably atleast about 98% identical, and more preferably at least about 99%identical to SEQ ID NO:5 or a domain thereof.

Another embodiment of the invention relates to an isolated homologue ofa protein represented by SEQ ID NO:6 that comprises, consistsessentially of, or consists of, an amino acid sequence that is at leastabout 60% identical to SEQ ID NO:6 or to a biologically active domainwithin SEQ ID NO:6 as previously described herein, wherein the homologuehas a biological activity of at least one domain that is containedwithin the corresponding protein represented by SEQ ID NO:6. Inadditional embodiments, the homologue is at least about 65% identical,and more preferably at least about 70% identical, and more preferably atleast about 75% identical, and more preferably at least about 80%identical, and more preferably at least about 85% identical, and morepreferably at least about 90% identical, and more preferably at leastabout 95% identical, and more preferably at least about 96% identical,and more preferably at least about 97% identical, and more preferably atleast about 98% identical, and more preferably at least about 99%identical (or any percentage between 60% and 99%, in whole singlepercentage increments) to SEQ ID NO:6 or a domain thereof.

Another embodiment of the invention relates to an isolated homologue ofa protein represented by SEQ ID NO:8 that comprises, consistsessentially of, or consists of, an amino acid sequence that is at leastabout 65% identical to SEQ ID NO:8 or to a biologically active domainwithin SEQ ID NO:8 as previously described herein, wherein the homologuehas a biological activity of at least one domain that is containedwithin the corresponding protein represented by SEQ ID NO:8. Inadditional embodiments, the homologue is at least about 70% identical,and more preferably at least about 75% identical, and more preferably atleast about 80% identical, and more preferably at least about 85%identical, and more preferably at least about 90% identical, and morepreferably at least about 95% identical, and more preferably at leastabout 96% identical, and more preferably at least about 97% identical,and more preferably at least about 98% identical, and more preferably atleast about 99% identical (or any percentage between 60% and 99%, inwhole single percentage increments) to SEQ ID NO:8 or a domain thereof.

Another embodiment of the invention relates to an isolated homologue ofa protein represented by SEQ ID NO:9 that comprises, consistsessentially of, or consists of, an amino acid sequence that is at leastabout 60% identical to SEQ ID NO:9 or to a biologically active domainwithin SEQ ID NO:9 as previously described herein, wherein the homologuehas a biological activity of at least one domain that is containedwithin the corresponding protein represented by SEQ ID NO:9. Inadditional embodiments, the homologue is at least about 65% identical,and more preferably at least about 70% identical, and more preferably atleast about 75% identical, and more preferably at least about 80%identical, and more preferably at least about 85% identical, and morepreferably at least about 90% identical, and more preferably at leastabout 95% identical, and more preferably at least about 96% identical,and more preferably at least about 97% identical, and more preferably atleast about 98% identical, and more preferably at least about 99%identical (or any percentage between 60% and 99%, in whole singlepercentage increments) to SEQ ID NO:9 or a domain thereof.

Another embodiment of the invention relates to an isolated homologue ofa protein represented by SEQ ID NO:10 that comprises, consistsessentially of, or consists of, an amino acid sequence that is at leastabout 70% identical to SEQ ID NO:10 or to a biologically active domainwithin SEQ ID NO:10 as previously described herein, wherein thehomologue has a biological activity of at least one domain that iscontained within the corresponding protein represented by SEQ ID NO:10.In additional embodiments, the homologue is at least about 75%identical, and more preferably at least about 80% identical, and morepreferably at least about 85% identical, and more preferably at leastabout 90% identical, and more preferably at least about 95% identical,and more preferably at least about 96% identical, and more preferably atleast about 97% identical, and more preferably at least about 98%identical, and more preferably at least about 99% identical (or anypercentage between 60% and 99%, in whole single percentage increments)to SEQ ID NO:10 or a domain thereof.

Another embodiment of the invention relates to an isolated homologue ofa protein represented by SEQ ID NO:11 that comprises, consistsessentially of, or consists of, an amino acid sequence that is at leastabout 85% identical to SEQ ID NO:11 or to a biologically active domainwithin SEQ ID NO:11 as previously described herein, wherein thehomologue has a biological activity of at least one domain that iscontained within the corresponding protein represented by SEQ ID NO:11.In additional embodiments, the homologue is at least about 90%identical, and more preferably at least about 95% identical, and morepreferably at least about 96% identical, and more preferably at leastabout 97% identical, and more preferably at least about 98% identical,and more preferably at least about 99% identical (or any percentagebetween 60% and 99%, in whole single percentage increments) to SEQ IDNO:11 or a domain thereof.

Another embodiment of the invention relates to an isolated homologue ofa protein represented by SEQ ID NO:12 that comprises, consistsessentially of, or consists of, an amino acid sequence that is at leastabout 60% identical to SEQ ID NO:12 or to a biologically active domainwithin SEQ ID NO:12 as previously described herein, wherein thehomologue has a biological activity of at least one domain that iscontained within the corresponding protein represented by SEQ ID NO:12.In additional embodiments, the homologue is at least about 65%identical, and more preferably at least about 70% identical, and morepreferably at least about 75% identical, and more preferably at leastabout 80% identical, and more preferably at least about 85% identical,and more preferably at least about 90% identical, and more preferably atleast about 95% identical, and more preferably at least about 96%identical, and more preferably at least about 97% identical, and morepreferably at least about 98% identical, and more preferably at leastabout 99% identical (or any percentage between 60% and 99%, in wholesingle percentage increments) to SEQ ID NO:12 or a domain thereof.

In one aspect of the invention, a PUFA PKS protein or domain encompassedby the present invention, including a homologue of a particular PUFA PKSprotein or domain described herein, comprises an amino acid sequencethat includes at least about 100 consecutive amino acids of the aminoacid sequence chosen from any one of SEQ ID NOs:2-6 or 8-12, wherein theamino acid sequence of the homologue has a biological activity of atleast one domain or protein as described herein. In a further aspect,the amino acid sequence of the protein is comprises at least about 200consecutive amino acids, and more preferably at least about 300consecutive amino acids, and more preferably at least about 400consecutive amino acids, and more preferably at least about 500consecutive amino acids, and more preferably at least about 600consecutive amino acids, and more preferably at least about 700consecutive amino acids, and more preferably at least about 800consecutive amino acids, and more preferably at least about 900consecutive amino acids, and more preferably at least about 1000consecutive amino acids of any of SEQ ID NOs:2-6 or 8-12.

In a preferred embodiment of the present invention, an isolated proteinor domain of the present invention comprises, consists essentially of,or consists of, an amino acid sequence chosen from: SEQ ID NO:2, SEQ IDNO:3, SEQ ID NO:4, SEQ ID NO:5, SEQ ID NO:6, SEQ ID NO:8, SEQ ID NO:9,SEQ ID NO:10, SEQ ID NO:11, SEQ ID NO:12, or any biologically activefragments or domains thereof.

In one embodiment, a biologically active domain of a PUFA PKS system asdescribed herein and referenced above comprises, consists essentiallyof, or consists of, an amino acid sequence chosen from: (1) from aboutposition 29 to about position 513 of SEQ ID NO:2, wherein the domain hasKS biological activity; (2) from about position 625 to about position943 of SEQ ID NO:2, wherein the domain has MAT biological activity; (3)from about position 1264 to about position 1889 of SEQ ID NO:2, andsubdomains thereof, wherein the domain or subdomain thereof has ACPbiological activity; (4) from about position 2264 to about position 2398of SEQ ID NO:2, wherein the domain has KR biological activity; (5) asequence comprising from about position 2504 to about position 2516 ofSEQ ID NO:2, wherein the domain has DH biological activity, andpreferably, non-FabA-like DH activity; (6) from about position 378 toabout position 684 of SEQ ID NO:3, wherein the domain has AT biologicalactivity; (7) from about position 5 to about position 483 of SEQ IDNO:4, wherein the domain has KS biological activity; (8) from aboutposition 489 to about position 771 of SEQ ID NO:4, wherein the domainhas CLF biological activity; (9) from about position 1428 to aboutposition 1570 of SEQ ID NO:4, wherein the domain has DH biologicalactivity, and preferably, FabA-like DH activity; (10) from aboutposition 1881 to about position 2019 of SEQ ID NO:4, wherein the domainhas DH biological activity, and preferably, FabA-like DH activity; (11)from about position 84 to about position 497 of SEQ ID NO:5, wherein thedomain has ER biological activity; (12) from about position 40 to aboutposition 186 of SEQ ID NO:6, wherein the domain has PPTase biologicalactivity; (13) from about position 29 to about position 513 of SEQ IDNO:8, wherein the domain has KS biological activity; (14) from aboutposition 625 to about position 943 of SEQ ID NO:8, wherein the domainhas MAT biological activity; (15) from about position 1275 to aboutposition 1872 of SEQ ID NO:8, and subdomains thereof, wherein the domainor subdomain thereof has ACP biological activity; (16) from aboutposition 2240 to about position 2374 of SEQ ID NO:8, wherein the domainhas KR biological activity; (17) a sequence comprising from aboutposition 2480-2492 of SEQ ID NO:8, wherein the sequence has DHbiological activity, and preferably, non-FabA-like DH activity; (18)from about position 366 to about position 703 of SEQ ID NO:9, whereinthe domain has AT biological activity; (19) from about position 10 toabout position 488 of SEQ ID NO:10, wherein the domain has KS biologicalactivity; (20) from about position 502 to about position 750 of SEQ IDNO:10, wherein the domain has CLF biological activity; (21) from aboutposition 1431 to about position 1573 of SEQ ID NO:10, wherein the domainhas DH biological activity, and preferably, FabA-like DH activity; (22)from about position 1882 to about position 2020 of SEQ ID NO:10, whereinthe domain has DH biological activity, and preferably, FabA-like DHactivity; (23) from about position 84 to about position 497 of SEQ IDNO:11, wherein the domain has ER biological activity; or (24) from aboutposition 29 to about position 177 of SEQ ID NO:12, wherein the domainhas PPTase biological activity.

According to the present invention, the term “contiguous” or“consecutive”, with regard to nucleic acid or amino acid sequencesdescribed herein, means to be connected in an unbroken sequence. Forexample, for a first sequence to comprise 30 contiguous (or consecutive)amino acids of a second sequence, means that the first sequence includesan unbroken sequence of 30 amino acid residues that is 100% identical toan unbroken sequence of 30 amino acid residues in the second sequence.Similarly, for a first sequence to have “100% identity” with a secondsequence means that the first sequence exactly matches the secondsequence with no gaps between nucleotides or amino acids.

As used herein, unless otherwise specified, reference to a percent (%)identity refers to an evaluation of homology which is performed using:(1) a BLAST 2.0 Basic BLAST homology search using blastp for amino acidsearches, blastn for nucleic acid searches, and blastX for nucleic acidsearches and searches of translated amino acids in all 6 open readingframes, all with standard default parameters, wherein the query sequenceis filtered for low complexity regions by default (described inAltschul, S. F., Madden, T. L., Schääffer, A. A., Zhang, J., Zhang, Z.,Miller, W. & Lipman, D. J. (1997) “Gapped BLAST and PSI-BLAST: a newgeneration of protein database search programs.” Nucleic Acids Res.25:3389, incorporated herein by reference in its entirety); (2) a BLAST2 alignment (using the parameters described below); (3) and/or PSI-BLASTwith the standard default parameters (Position-Specific Iterated BLAST).It is noted that due to some differences in the standard parametersbetween BLAST 2.0 Basic BLAST and BLAST 2, two specific sequences mightbe recognized as having significant homology using the BLAST 2 program,whereas a search performed in BLAST 2.0 Basic BLAST using one of thesequences as the query sequence may not identify the second sequence inthe top matches. In addition, PSI-BLAST provides an automated,easy-to-use version of a “profile” search, which is a sensitive way tolook for sequence homologues. The program first performs a gapped BLASTdatabase search. The PSI-BLAST program uses the information from anysignificant alignments returned to construct a position-specific scorematrix, which replaces the query sequence for the next round of databasesearching. Therefore, it is to be understood that percent identity canbe determined by using any one of these programs.

Two specific sequences can be aligned to one another using BLAST 2sequence as described in Tatusova and Madden, “Blast 2 sequences—a newtool for comparing protein and nucleotide sequences”, FEMS MicrobiolLett. 174:247 (1999), incorporated herein by reference in its entirety.BLAST 2 sequence alignment is performed in blastp or blastn using theBLAST 2.0 algorithm to perform a Gapped BLAST search (BLAST 2.0) betweenthe two sequences allowing for the introduction of gaps (deletions andinsertions) in the resulting alignment. For purposes of clarity herein,a BLAST 2 sequence alignment is performed using the standard defaultparameters as follows.

For blastn, using 0 BLOSUM62 matrix:

-   -   Reward for match=1    -   Penalty for mismatch =−2    -   Open gap (5) and extension gap (2) penalties    -   gap x_dropoff (50) expect (10) word size (11) filter (on)        For blastp, using 0 BLOSUM62 matrix:    -   Open gap (11) and extension gap (1) penalties    -   gap x_dropoff (50) expect (10) word size (3) filter (on).

According to the present invention, an amino acid sequence that has abiological activity of at least one domain of a PUFA PKS system is anamino acid sequence that has the biological activity of at least onedomain of the PUFA PKS system described in detail herein (e.g., a KSdomain, an AT domain, a CLF domain, etc.). Therefore, an isolatedprotein useful in the present invention can include: the translationproduct of any PUFA PKS open reading frame, any PUFA PKS domain, anybiologically active fragment of such a translation product or domain, orany homologue of a naturally occurring PUFA PKS open reading frameproduct or domain which has biological activity.

In another embodiment of the invention, an amino acid sequence havingthe biological activity of at least one domain of a PUFA PKS system ofthe present invention includes an amino acid sequence that issufficiently similar to a naturally occurring PUFA PKS protein orpolypeptide that is specifically described herein that a nucleic acidsequence encoding the amino acid sequence is capable of hybridizingunder moderate, high, or very high stringency conditions (describedbelow) to (i.e., with) a nucleic acid molecule encoding the naturallyoccurring PUFA PKS protein or polypeptide (i.e., to the complement ofthe nucleic acid strand encoding the naturally occurring PUFA PKSprotein or polypeptide). Preferably, an amino acid sequence having thebiological activity of at least one domain of a PUFA PKS system of thepresent invention is encoded by a nucleic acid sequence that hybridizesunder moderate, high or very high stringency conditions to thecomplement of a nucleic acid sequence that encodes any of theabove-described amino acid sequences for a PUFA PKS protein or domain.Methods to deduce a complementary sequence are known to those skilled inthe art. It should be noted that since amino acid sequencing and nucleicacid sequencing technologies are not entirely error-free, the sequencespresented herein, at best, represent apparent sequences of PUFA PKSdomains and proteins of the present invention.

As used herein, hybridization conditions refer to standard hybridizationconditions under which nucleic acid molecules are used to identifysimilar nucleic acid molecules. Such standard conditions are disclosed,for example, in Sambrook et al., Molecular Cloning: A Laboratory Manual,Cold Spring Harbor Labs Press (1989). Sambrook et al., ibid., isincorporated by reference herein in its entirety (see specifically,pages 9.31-9.62). In addition, formulae to calculate the appropriatehybridization and wash conditions to achieve hybridization permittingvarying degrees of mismatch of nucleotides are disclosed, for example,in Meinkoth et al., Anal. Biochem. 138, 267 (1984); Meinkoth et al.,ibid., is incorporated by reference herein in its entirety.

More particularly, moderate stringency hybridization and washingconditions, as referred to herein, refer to conditions which permitisolation of nucleic acid molecules having at least about 70% nucleicacid sequence identity with the nucleic acid molecule being used toprobe in the hybridization reaction (i.e., conditions permitting about30% or less mismatch of nucleotides). High stringency hybridization andwashing conditions, as referred to herein, refer to conditions whichpermit isolation of nucleic acid molecules having at least about 80%nucleic acid sequence identity with the nucleic acid molecule being usedto probe in the hybridization reaction (i.e., conditions permittingabout 20% or less mismatch of nucleotides). Very high stringencyhybridization and washing conditions, as referred to herein, refer toconditions which permit isolation of nucleic acid molecules having atleast about 90% nucleic acid sequence identity with the nucleic acidmolecule being used to probe in the hybridization reaction (i.e.,conditions permitting about 10% or less mismatch of nucleotides). Asdiscussed above, one of skill in the art can use the formulae inMeinkoth et al., ibid. to calculate the appropriate hybridization andwash conditions to achieve these particular levels of nucleotidemismatch. Such conditions will vary, depending on whether DNA:RNA orDNA:DNA hybrids are being formed. Calculated melting temperatures forDNA:DNA hybrids are 10° C. less than for DNA:RNA hybrids. In particularembodiments, stringent hybridization conditions for DNA:DNA hybridsinclude hybridization at an ionic strength of 6×SSC (0.9 M Na⁺) at atemperature of between about 20° C. and about 35° C. (lower stringency),more preferably, between about 28° C. and about 40° C. (more stringent),and even more preferably, between about 35° C. and about 45° C. (evenmore stringent), with appropriate wash conditions. In particularembodiments, stringent hybridization conditions for DNA:RNA hybridsinclude hybridization at an ionic strength of 6×SSC (0.9 M Na⁺) at atemperature of between about 30° C. and about 45° C., more preferably,between about 38° C. and about 50° C., and even more preferably, betweenabout 45° C. and about 55° C., with similarly stringent wash conditions.These values are based on calculations of a melting temperature formolecules larger than about 100 nucleotides, 0% formamide and a G+Ccontent of about 40%. Alternatively, T_(m) can be calculated empiricallyas set forth in Sambrook et al., supra, pages 9.31 to 9.62. In general,the wash conditions should be as stringent as possible, and should beappropriate for the chosen hybridization conditions. For example,hybridization conditions can include a combination of salt andtemperature conditions that are approximately 20-25° C. below thecalculated T_(m) of a particular hybrid, and wash conditions typicallyinclude a combination of salt and temperature conditions that areapproximately 12-20° C. below the calculated T_(m) of the particularhybrid. One example of hybridization conditions suitable for use withDNA:DNA hybrids includes a 2-24 hour hybridization in 6×SSC (50%formamide) at about 42° C., followed by washing steps that include oneor more washes at room temperature in about 2×SSC, followed byadditional washes at higher temperatures and lower ionic strength (e.g.,at least one wash as about 37° C. in about 0.1×-0.5×SSC, followed by atleast one wash at about 68° C. in about 0.1×-0.5×SSC).

The present invention also includes a fusion protein that includes anyPUFA PKS protein or domain or any homologue or fragment thereof attachedto one or more fusion segments. Suitable fusion segments for use withthe present invention include, but are not limited to, segments thatcan: enhance a protein's stability; provide other desirable biologicalactivity; and/or assist with the purification of the protein (e.g., byaffinity chromatography). A suitable fusion segment can be a domain ofany size that has the desired function (e.g., imparts increasedstability, solubility, biological activity; and/or simplifiespurification of a protein). Fusion segments can be joined to aminoand/or carboxyl termini of the protein and can be susceptible tocleavage in order to enable straight-forward recovery of the desiredprotein. Fusion proteins are preferably produced by culturing arecombinant cell transfected with a fusion nucleic acid molecule thatencodes a protein including the fusion segment attached to either thecarboxyl and/or amino terminal end of the protein of the invention asdiscussed above.

In one embodiment of the present invention, any of the above-describedPUFA PKS amino acid sequences, as well as homologues of such sequences,can be produced with from at least one, and up to about 20, additionalheterologous amino acids flanking each of the C- and/or N-terminal endof the given amino acid sequence. The resulting protein or polypeptidecan be referred to as “consisting essentially of” a given amino acidsequence. According to the present invention, the heterologous aminoacids are a sequence of amino acids that are not naturally found (i.e.,not found in nature, in vivo) flanking the given amino acid sequence orwhich would not be encoded by the nucleotides that flank the naturallyoccurring nucleic acid sequence encoding the given amino acid sequenceas it occurs in the gene, if such nucleotides in the naturally occurringsequence were translated using standard codon usage for the organismfrom which the given amino acid sequence is derived. Similarly, thephrase “consisting essentially of”, when used with reference to anucleic acid sequence herein, refers to a nucleic acid sequence encodinga given amino acid sequence that can be flanked by from at least one,and up to as many as about 60, additional heterologous nucleotides ateach of the 5′ and/or the 3′ end of the nucleic acid sequence encodingthe given amino acid sequence. The heterologous nucleotides are notnaturally found (i.e., not found in nature, in vivo) flanking thenucleic acid sequence encoding the given amino acid sequence as itoccurs in the natural gene.

The minimum size of a protein or domain and/or a homologue or fragmentthereof of the present invention is, in one aspect, a size sufficient tohave the requisite biological activity, or sufficient to serve as anantigen for the generation of an antibody or as a target in an in vitroassay. In one embodiment, a protein of the present invention is at leastabout 8 amino acids in length (e.g., suitable for an antibody epitope oras a detectable peptide in an assay), or at least about 25 amino acidsin length, or at least about 50 amino acids in length, or at least about100 amino acids in length, or at least about 150 amino acids in length,or at least about 200 amino acids in length, or at least about 250 aminoacids in length, or at least about 300 amino acids in length, or atleast about 350 amino acids in length, or at least about 400 amino acidsin length, or at least about 450 amino acids in length, or at leastabout 500 amino acids in length, and so on, in any length between 8amino acids and up to the full length of a protein or domain of theinvention or longer, in whole integers (e.g., 8, 9, 10, . . . 25, 26, .. . 500, 501, . . . ). There is no limit, other than a practical limit,on the maximum size of such a protein in that the protein can include aportion of a PUFA PKS protein, domain, or biologically active or usefulfragment thereof, or a full-length PUFA PKS protein or domain, plusadditional sequence (e.g., a fusion protein sequence), if desired.

One embodiment of the present invention relates to isolated nucleic acidmolecules comprising, consisting essentially of, or consisting ofnucleic acid sequences that encode any of the PUFA PKS proteins ordomains described herein, including a homologue or fragment of any ofsuch proteins or domains, as well as nucleic acid sequences that arefully complementary thereto. In accordance with the present invention,an isolated nucleic acid molecule is a nucleic acid molecule that hasbeen removed from its natural milieu (i.e., that has been subject tohuman manipulation), its natural milieu being the genome or chromosomein which the nucleic acid molecule is found in nature. As such,“isolated” does not necessarily reflect the extent to which the nucleicacid molecule has been purified, but indicates that the molecule doesnot include an entire genome or an entire chromosome in which thenucleic acid molecule is found in nature. An isolated nucleic acidmolecule can include a gene. An isolated nucleic acid molecule thatincludes a gene is not a fragment of a chromosome that includes suchgene, but rather includes the coding region and regulatory regionsassociated with the gene, but no additional genes that are naturallyfound on the same chromosome, with the exception of other genes thatencode other proteins of the PUFA PKS system as described herein. Anisolated nucleic acid molecule can also include a specified nucleic acidsequence flanked by (i.e., at the 5′ and/or the 3′ end of the sequence)additional nucleic acids that do not normally flank the specifiednucleic acid sequence in nature (i.e., heterologous sequences). Isolatednucleic acid molecule can include DNA, RNA (e.g., mRNA), or derivativesof either DNA or RNA (e.g., cDNA). Although the phrase “nucleic acidmolecule” primarily refers to the physical nucleic acid molecule and thephrase “nucleic acid sequence” primarily refers to the sequence ofnucleotides on the nucleic acid molecule, the two phrases can be usedinterchangeably, especially with respect to a nucleic acid molecule, ora nucleic acid sequence, being capable of encoding a protein or domainof a protein.

Preferably, an isolated nucleic acid molecule of the present inventionis produced using recombinant DNA technology (e.g., polymerase chainreaction (PCR) amplification, cloning) or chemical synthesis. Isolatednucleic acid molecules include natural nucleic acid molecules andhomologues thereof, including, but not limited to, natural allelicvariants and modified nucleic acid molecules in which nucleotides havebeen inserted, deleted, substituted, and/or inverted in such a mannerthat such modifications provide the desired effect on PUFA PKS systembiological activity as described herein. Protein homologues (e.g.,proteins encoded by nucleic acid homologues) have been discussed indetail above.

A nucleic acid molecule homologue can be produced using a number ofmethods known to those skilled in the art (see, for example, Sambrook etal., Molecular Cloning: A Laboratory Manual, Cold Spring Harbor LabsPress (1989)). For example, nucleic acid molecules can be modified usinga variety of techniques including, but not limited to, classicmutagenesis techniques and recombinant DNA techniques, such assite-directed mutagenesis, chemical treatment of a nucleic acid moleculeto induce mutations, restriction enzyme cleavage of a nucleic acidfragment, ligation of nucleic acid fragments, PCR amplification and/ormutagenesis of selected regions of a nucleic acid sequence, synthesis ofoligonucleotide mixtures and ligation of mixture groups to “build” amixture of nucleic acid molecules and combinations thereof. Nucleic acidmolecule homologues can be selected from a mixture of modified nucleicacids by screening for the function of the protein encoded by thenucleic acid and/or by hybridization with a wild-type gene.

The minimum size of a nucleic acid molecule of the present invention isa size sufficient to form a probe or oligonucleotide primer that iscapable of forming a stable hybrid (e.g., under moderate, high or veryhigh stringency conditions) with the complementary sequence of a nucleicacid molecule of the present invention, or of a size sufficient toencode an amino acid sequence having a biological activity of at leastone domain of a PUFA PKS system according to the present invention. Assuch, the size of the nucleic acid molecule encoding such a protein canbe dependent on nucleic acid composition and percent homology oridentity between the nucleic acid molecule and complementary sequence aswell as upon hybridization conditions per se (e.g., temperature, saltconcentration, and formamide concentration). The minimal size of anucleic acid molecule that is used as an oligonucleotide primer or as aprobe is typically at least about 12 to about 15 nucleotides in lengthif the nucleic acid molecules are GC-rich and at least about 15 to about18 bases in length if they are AT-rich. There is no limit, other than apractical limit, on the maximal size of a nucleic acid molecule of thepresent invention, in that the nucleic acid molecule can include asequence sufficient to encode a biologically active fragment of a domainof a PUFA PKS system, an entire domain of a PUFA PKS system, severaldomains within an open reading frame (Orf) of a PUFA PKS system, anentire single- or multi-domain protein of a PUFA PKS system, or morethan one protein of a PUFA PKS system.

In one embodiment of the present invention, an isolated nucleic acidmolecule comprises, consists essentially of, or consists of a nucleicacid sequence encoding any of the above-described amino acid sequences,including any of the amino acid sequences, or homologues thereof, fromShewanella japonica or Shewanella olleyana described herein. In oneaspect, the nucleic acid sequence is selected from the group of: SEQ IDNO:1 or SEQ ID NO:7 or any fragment (segment, portion) of SEQ ID NO:1 orSEQ ID NO:7 that encodes one or more domains or proteins of the PUFA PKSsystems described herein. In another aspect, the nucleic acid sequenceincludes any homologues of SEQ ID NO:1 or SEQ ID NO:7 or any fragment ofSEQ ID NO:1 or SEQ ID NO:7 that encodes one or more domains or proteinsof the PUFA PKS systems described herein (including sequences that areat least about 50%, 55%, 60%, 65%, 70%, 75%, 80%, 85%, 90%, 95%, 96%,97%, 98%, or 99% identical to such sequences). In yet another aspect,fragments and any complementary sequences of such nucleic acid sequencesare encompassed by the invention.

Another embodiment of the present invention includes a recombinantnucleic acid molecule comprising a recombinant vector and a nucleic acidsequence encoding protein or peptide having a biological activity of atleast one domain (or homologue or fragment thereof) of a PUFA PKSprotein as described herein. Such nucleic acid sequences are describedin detail above. According to the present invention, a recombinantvector is an engineered (i.e., artificially produced) nucleic acidmolecule that is used as a tool for manipulating a nucleic acid sequenceof choice and for introducing such a nucleic acid sequence into a hostcell. The recombinant vector is therefore suitable for use in cloning,sequencing, and/or otherwise manipulating the nucleic acid sequence ofchoice, such as by expressing and/or delivering the nucleic acidsequence of choice into a host cell to form a recombinant cell. Such avector typically contains heterologous nucleic acid sequences, that isnucleic acid sequences that are not naturally found adjacent to nucleicacid sequence to be cloned or delivered, although the vector can alsocontain regulatory nucleic acid sequences (e.g., promoters, untranslatedregions) which are naturally found adjacent to nucleic acid molecules ofthe present invention or which are useful for expression of the nucleicacid molecules of the present invention (discussed in detail below). Thevector can be either RNA or DNA, either prokaryotic or eukaryotic, andtypically is a plasmid. The vector can be maintained as anextrachromosomal element (e.g., a plasmid) or it can be integrated intothe chromosome of a recombinant organism (e.g., a microbe or a plant).The entire vector can remain in place within a host cell, or undercertain conditions, the plasmid DNA can be deleted, leaving behind thenucleic acid molecule of the present invention. The integrated nucleicacid molecule can be under chromosomal promoter control, under native orplasmid promoter control, or under a combination of several promotercontrols. Single or multiple copies of the nucleic acid molecule can beintegrated into the chromosome. A recombinant vector of the presentinvention can contain at least one selectable marker.

In one embodiment, a recombinant vector used in a recombinant nucleicacid molecule of the present invention is an expression vector. As usedherein, the phrase “expression vector” is used to refer to a vector thatis suitable for production of an encoded product (e.g., a protein ofinterest). In this embodiment, a nucleic acid sequence encoding theproduct to be produced (e.g., a PUFA PKS domain or protein) is insertedinto the recombinant vector to produce a recombinant nucleic acidmolecule. The nucleic acid sequence encoding the protein to be producedis inserted into the vector in a manner that operatively links thenucleic acid sequence to regulatory sequences in the vector that enablethe transcription and translation of the nucleic acid sequence withinthe recombinant host cell.

In another embodiment, a recombinant vector used in a recombinantnucleic acid molecule of the present invention is a targeting vector. Asused herein, the phrase “targeting vector” is used to refer to a vectorthat is used to deliver a particular nucleic acid molecule into arecombinant host cell, wherein the nucleic acid molecule is used todelete, inactivate, or replace an endogenous gene or portion of a genewithin the host cell or microorganism (i.e., used for targeted genedisruption or knock-out technology). Such a vector may also be known inthe art as a “knock-out” vector. In one aspect of this embodiment, aportion of the vector, but more typically, the nucleic acid moleculeinserted into the vector (i.e., the insert), has a nucleic acid sequencethat is homologous to a nucleic acid sequence of a target gene in thehost cell (i.e., a gene which is targeted to be deleted or inactivated).The nucleic acid sequence of the vector insert is designed to associatewith the target gene such that the target gene and the insert mayundergo homologous recombination, whereby the endogenous target gene isdeleted, inactivated, attenuated (i.e., by at least a portion of theendogenous target gene being mutated or deleted), or replaced. The useof this type of recombinant vector to replace an endogenousSchizochytrium gene, for example, with a recombinant gene is describedin the Examples section, and the general technique for genetictransformation of Thraustochytrids is described in detail in U.S. patentapplication Ser. No. 10/124,807, published as U.S. Patent ApplicationPublication No. 20030166207, published Sep. 4, 2003. Genetictransformation techniques for plants are well-known in the art. It is anembodiment of the present invention that the marine bacterial genesdescribed herein can be used to transform plants or microorganisms suchas Thraustochytrids to improve and/or alter (modify, change) the PUFAPKS production capabilities of such plants or microorganisms.

Typically, a recombinant nucleic acid molecule includes at least onenucleic acid molecule of the present invention operatively linked to oneor more expression control sequences. As used herein, the phrase“recombinant molecule” or “recombinant nucleic acid molecule” primarilyrefers to a nucleic acid molecule or nucleic acid sequence operativelylinked to a expression control sequence, but can be used interchangeablywith the phrase “nucleic acid molecule”, when such nucleic acid moleculeis a recombinant molecule as discussed herein. According to the presentinvention, the phrase “operatively linked” refers to linking a nucleicacid molecule to an expression control sequence (e.g., a transcriptioncontrol sequence and/or a translation control sequence) in a manner suchthat the molecule can be expressed when transfected (i.e., transformed,transduced, transfected, conjugated or conduced) into a host cell.Transcription control sequences are sequences that control theinitiation, elongation, or termination of transcription. Particularlyimportant transcription control sequences are those that controltranscription initiation, such as promoter, enhancer, operator andrepressor sequences. Suitable transcription control sequences includeany transcription control sequence that can function in a host cell ororganism into which the recombinant nucleic acid molecule is to beintroduced.

Recombinant nucleic acid molecules of the present invention can alsocontain additional regulatory sequences, such as translation regulatorysequences, origins of replication, and other regulatory sequences thatare compatible with the recombinant cell. In one embodiment, arecombinant molecule of the present invention, including those that areintegrated into the host cell chromosome, also contains secretorysignals (i.e., signal segment nucleic acid sequences) to enable anexpressed protein to be secreted from the cell that produces theprotein. Suitable signal segments include a signal segment that isnaturally associated with the protein to be expressed or anyheterologous signal segment capable of directing the secretion of theprotein according to the present invention. In another embodiment, arecombinant molecule of the present invention comprises a leadersequence to enable an expressed protein to be delivered to and insertedinto the membrane of a host cell. Suitable leader sequences include aleader sequence that is naturally associated with the protein, or anyheterologous leader sequence capable of directing the delivery andinsertion of the protein to the membrane of a cell.

One or more recombinant molecules of the present invention can be usedto produce an encoded product (e.g., a PUFA PKS domain, protein, orsystem) of the present invention. In one embodiment, an encoded productis produced by expressing a nucleic acid molecule as described hereinunder conditions effective to produce the protein. A preferred method toproduce an encoded protein is by transfecting a host cell with one ormore recombinant molecules to form a recombinant cell. Suitable hostcells to transfect include, but are not limited to, any bacterial,fungal (e.g., yeast), insect, plant or animal cell that can betransfected. In one embodiment of the invention, a preferred host cellis a Thraustochytrid host cell (described in detail below) or a planthost cell. Host cells can be either untransfected cells or cells thatare already transfected with at least one other recombinant nucleic acidmolecule.

According to the present invention, the term “transfection” is used torefer to any method by which an exogenous nucleic acid molecule (i.e., arecombinant nucleic acid molecule) can be inserted into a cell. The term“transformation” can be used interchangeably with the term“transfection” when such term is used to refer to the introduction ofnucleic acid molecules into microbial cells, such as algae, bacteria andyeast, or into plant cells. In microbial and plant systems, the term“transformation” is used to describe an inherited change due to theacquisition of exogenous nucleic acids by the microorganism or plant andis essentially synonymous with the term “transfection.” However, inanimal cells, transformation has acquired a second meaning which canrefer to changes in the growth properties of cells in culture after theybecome cancerous, for example. Therefore, to avoid confusion, the term“transfection” is preferably used with regard to the introduction ofexogenous nucleic acids into animal cells, and the term “transfection”will be used herein to generally encompass transfection of animal cells,and transformation of microbial cells or plant cells, to the extent thatthe terms pertain to the introduction of exogenous nucleic acids into acell. Therefore, transfection techniques include, but are not limitedto, transformation, particle bombardment, diffusion, active transport,bath sonication, electroporation, microinjection, lipofection,adsorption, infection and protoplast fusion.

It will be appreciated by one skilled in the art that use of recombinantDNA technologies can improve control of expression of transfectednucleic acid molecules by manipulating, for example, the number ofcopies of the nucleic acid molecules within the host cell, theefficiency with which those nucleic acid molecules are transcribed, theefficiency with which the resultant transcripts are translated, and theefficiency of post-translational modifications. Additionally, thepromoter sequence might be genetically engineered to improve the levelof expression as compared to the native promoter. Recombinant techniquesuseful for controlling the expression of nucleic acid molecules include,but are not limited to, integration of the nucleic acid molecules intoone or more host cell chromosomes, addition of vector stabilitysequences to plasmids, substitutions or modifications of transcriptioncontrol signals (e.g., promoters, operators, enhancers), substitutionsor modifications of translational control signals (e.g., ribosomebinding sites, Shine-Dalgamo sequences), modification of nucleic acidmolecules to correspond to the codon usage of the host cell, anddeletion of sequences that destabilize transcripts.

General discussion above with regard to recombinant nucleic acidmolecules and transfection of host cells is intended to be applied toany recombinant nucleic acid molecule discussed herein, including thoseencoding any amino acid sequence having a biological activity of atleast one domain from a PUFA PKS system, those encoding amino acidsequences from other PKS systems, and those encoding other proteins ordomains.

Polyunsaturated fatty acids (PUFAs) are essential membrane components inhigher eukaryotes and the precursors of many lipid-derived signalingmolecules. The PUFA PKS system of the present invention uses pathwaysfor PUFA synthesis that do not require desaturation and elongation ofsaturated fatty acids. The pathways catalyzed by PUFA PKS systems aredistinct from previously recognized PKS systems in both structure andmechanism. Generation of cis double bonds is suggested to involveposition-specific isomerases; these enzymes are believed to be useful inthe production of new families of antibiotics.

To produce significantly high yields of one or more desiredpolyunsaturated fatty acids or other bioactive molecules, an organism,preferably a microorganism or a plant, can be genetically modified toalter the activity and particularly, the end product, of the PUFA PKSsystem in the microorganism or plant or to introduce a PUFA PKS systeminto the microorganism or plant.

Therefore, one embodiment of the present invention relates to agenetically modified microorganism, wherein the microorganism expressesa PKS system comprising at least one biologically active domain of apolyunsaturated fatty acid (PUFA) polyketide synthase (PKS) system asdescribed herein (e.g., at least one domain or protein, or biologicallyactive fragment or homologue thereof, of a PUFA PKS system fromShewanella japonica or Shewanella olleyana). The genetic modification ofthe microorganism affects the activity of the PKS system in theorganism. The domain of the PUFA PKS system can include any of thedomains, including homologues thereof, for the marine bacterial PUFA PKSsystems as described above, and can also include any domain of a PUFAPKS system from any other bacterial or non-bacterial microorganism,including any eukaryotic microorganism, and particularly including anyThraustochytrid microorganism or any domain of a PUFA PKS system from amicroorganism identified by a screening method as described in U.S.patent application Ser. No. 10/124,800, supra. Briefly, the screeningprocess described in U.S. patent application Ser. No. 10/124,800includes the steps of: (a) selecting a microorganism that produces atleast one PUFA; and, (b) identifying a microorganism from (a) that hasan ability to produce increased PUFAs under dissolved oxygen conditionsof less than about 5% of saturation in the fermentation medium, ascompared to production of PUFAs by the microorganism under dissolvedoxygen conditions of greater than about 5% of saturation, and preferablyabout 10%, and more preferably about 15%, and more preferably about 20%of saturation in the fermentation medium. Proteins, domains, andhomologues thereof for other bacterial PUFA PKS systems are described inU.S. Pat. No. 6,140,486, supra, incorporated by reference in itsentirety. Proteins, domains, and homologues thereof for ThraustochytridPUFA PKS systems are described in detail in U.S. Pat. No. 6,566,583,supra; U.S. patent application Ser. No. 10/124,800, supra; and U.S.patent application Ser. No. 10/810,352, supra, each of which isincorporated herein by reference in its entirety.

In one aspect of the invention, a genetically modified organism canendogenously contain and express a PUFA PKS system, and the geneticmodification can be a genetic modification of one or more of thefunctional domains of the endogenous PUFA PKS system, whereby themodification has some effect on the activity of the PUFA PKS system. Forexample, the Shewanella japonica or Shewanella olleyana speciesdescribed herein may be genetically modified by modifying an endogenousPUFA PKS gene or genes that results in some alteration (change,modification) of the PUFA PKS function in that microorganism.

In another aspect of the invention, a genetically modified organism canendogenously contain and express a PUFA PKS system, and the geneticmodification can be an introduction of at least one exogenous nucleicacid sequence (e.g., a recombinant nucleic acid molecule), wherein theexogenous nucleic acid sequence encodes at least one biologically activedomain or protein from a second PKS system (including a PUFA PKS systemor another type of PKS system) and/or a protein that affects theactivity of the PUFA PKS system. In this aspect of the invention, theorganism can also have at least one modification to a gene or genescomprising its endogenous PUFA PKS system.

In yet another aspect of the invention, the genetically modifiedorganism does not necessarily endogenously (naturally) contain a PUFAPKS system, but is genetically modified to introduce at least onerecombinant nucleic acid molecule encoding an amino acid sequence havingthe biological activity of at least one domain of a PUFA PKS system.Preferably, the organism is genetically modified to introduce more thanone recombinant nucleic acid molecule which together encode therequisite components of a PUFA PKS system for production of a PUFA PKSsystem product (bioactive molecule, such as a PUFA or antibiotic), or tointroduce a recombinant nucleic acid molecule encoding multiple domainscomprising the requisite components of a PUFA PKS system for productionof a PUFA PKS product. Various embodiments associated with each of theseaspects will be discussed in greater detail below.

It is to be understood that a genetic modification of a PUFA PKS systemor an organism comprising a PUFA PKS system can involve the modificationand/or utilization of at least one domain of a PUFA PKS system(including a portion of a domain), more than one or several domains of aPUFA PKS system (including adjacent domains, non-contiguous domains, ordomains on different proteins in the PUFA PKS system), entire proteinsof the PUFA PKS system, and the entire PUFA PKS system (e.g., all of theproteins encoded by the PUFA PKS genes) or even more than one PUFA PKSsystem (e.g., one from an organism that naturally produces DHA and onefrom an organism that naturally produces EPA). As such, modificationscan include, but are not limited to: a small modification to a singledomain of an endogenous PUFA PKS system; substitution of, deletion of oraddition to one or more domains or proteins of an endogenous PUFA PKSsystem; introduction of one or more domains or proteins from arecombinant PUFA PKS system; introduction of a second PUFA PKS system inan organism with an endogenous PUFA PKS system; replacement of theentire PUFA PKS system in an organism with the PUFA PKS system from adifferent organism; or introduction of one, two, or more entire PUFA PKSsystems to an organism that does not endogenously have a PUFA PKSsystem. One of skill in the art will understand that any geneticmodification to a PUFA PKS system is encompassed by the invention.

As used herein, a genetically modified microorganism can include agenetically modified bacterium, protist, microalgae, fungus, or othermicrobe, and particularly, any of the genera of the orderThraustochytriales (e.g., a Thraustochytrid), including anymicroorganism in the families Thraustochytriaceae and Labyrinthulaceaedescribed herein (e.g., Schizochytrium, Thraustochytrium,Japonochytrium, Labyrinthula, Labyrinthuloides, etc.). Such agenetically modified microorganism has a genome which is modified (i.e.,mutated or changed) from its normal (i.e., wild-type or naturallyoccurring) form such that the desired result is achieved (i.e.,increased or modified PUFA PKS activity and/or production of a desiredproduct using the PKS system). Genetic modification of a microorganismcan be accomplished using classical strain development and/or moleculargenetic techniques. Such techniques known in the art and are generallydisclosed for microorganisms, for example, in Sambrook et al., 1989,Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Labs Press.The reference Sambrook et al., ibid., is incorporated by referenceherein in its entirety. A genetically modified microorganism can includea microorganism in which nucleic acid molecules have been inserted,deleted or modified (i.e., mutated; e.g., by insertion, deletion,substitution, and/or inversion of nucleotides), in such a manner thatsuch modifications provide the desired effect within the microorganism.

Examples of suitable host microorganisms for genetic modificationinclude, but are not limited to, yeast including Saccharomycescerevisiae, Saccharomyces carlsbergensis, or other yeast such asCandida, Kluyveromyces, or other fungi, for example, filamentous fungisuch as Aspergillus, Neurospora, Penicillium, etc. Bacterial cells alsomay be used as hosts. These include, but are not limited to, Escherichiacoli, which can be useful in fermentation processes. Alternatively, andonly by way of example, a host such as a Lactobacillus species orBacillus species can be used as a host.

Particularly preferred host cells for use in the present inventioninclude microorganisms from a genus including, but not limited to:Thraustochytrium, Japonochytrium, Aplanochytrium, Elina andSchizochytrium within the Thraustochytriaceae, and Labyrinthula,Labyrinthuloides, and Labyrinthomyxa within the Labyrinthulaceae.Preferred species within these genera include, but are not limited to:any species within Labyrinthula, including Labyrinthula sp.,Labyrinthula algeriensis, Labyrinthula cienkowskii, Labyrinthulachattonii, Labyrinthula coenocystis, Labyrinthula macrocystis,Labyrinthula macrocystis atlantica, Labyrinthula macrocystismacrocystis, Labyrinthula magnifica, Labyrinthula minuta, Labyrinthularoscoffensis, Labyrinthula valkanovii, Labyrinthula vitellina,Labyrinthula vitellina pacifica, Labyrinthula vitellina vitellina,Labyrinthula zopfii; any Labyrinthuloides species, includingLabyrinthuloides sp., Labyrinthuloides minuta, Labyrinthuloidesschizochytrops; any Labyrinthomyxa species, including Labyrinthomyxasp., Labyrinthomyxa pohlia, Labyrinthomyxa sauvageaui, anyAplanochytrium species, including Aplanochytrium sp. and Aplanochytriumkerguelensis; any Elina species, including Elina sp., Elina marisalba,Elina sinorifica; any Japonochytrium species, including Japonochytriumsp., Japonochytrium marinum; any Schizochytrium species, includingSchizochytrium sp., Schizochytrium aggregatum, Schizochytrium limacinum,Schizochytrium minutum, Schizochytrium octosporum; and anyThraustochytrium species, including Thraustochytrium sp.,Thraustochytrium aggregatum, Thraustochytrium arudimentale,Thraustochytrium aureum, Thraustochytrium benthicola, Thraustochytriumglobosum, Thraustochytrium kinnei, Thraustochytrium motivum,Thraustochytrium pachydermum, Thraustochytrium proliferum,Thraustochytrium roseum, Thraustochytrium striatum, Ulkenia sp., Ulkeniaminuta, Ulkenia profunda, Ulkenia radiate, Ulkenia sarkariana, andUlkenia visurgensis. Particularly preferred species within these generainclude, but are not limited to: any Schizochytrium species, includingSchizochytrium aggregatum, Schizochytrium limacinum, Schizochytriumminutum; or any Thraustochytrium species (including former Ulkeniaspecies such as U. visurgensis, U. amoeboida, U. sarkariana, U.profunda, U. radiata, U. minuta and Ulkenia sp. BP-5601), and includingThraustochytrium striatum, Thraustochytrium aureum, Thraustochytriumroseum; and any Japonochytrium species. Particularly preferred strainsof Thraustochytriales include, but are not limited to: Schizochytriumsp. (S31) (ATCC 20888); Schizochytrium sp. (S8) (ATCC 20889);Schizochytrium sp. (LC-RM) (ATCC 18915); Schizochytrium sp. (SR21);Schizochytrium aggregatum (Goldstein et Belsky) (ATCC 28209);Schizochytrium limacinum (Honda et Yokochi) (IFO 32693);Thraustochytrium sp. (23B) (ATCC 20891); Thraustochytrium striatum(Schneider) (ATCC 24473); Thraustochytrium aureum (Goldstein) (ATCC34304); Thraustochytrium roseum (Goldstein) (ATCC 28210); andJaponochytrium sp. (L1) (ATCC 28207).

According to the present invention, the terms/phrases “Thraustochytrid”,“Thraustochytriales microorganism” and “microorganism of the orderThraustochytriales” can be used interchangeably and refer to any membersof the order Thraustochytriales, which includes both the familyThraustochytriaceae and the family Labyrinthulaceae. The terms“Labyrinthulid” and “Labyrinthulaceae” are used herein to specificallyrefer to members of the family Labyrinthulaceae. To specificallyreference Thraustochytrids that are members of the familyThraustochytriaceae, the term “Thraustochytriaceae” is used herein.Thus, for the present invention, members of the Labyrinthulids areconsidered to be included in the Thraustochytrids.

Developments have resulted in frequent revision of the taxonomy of theThraustochytrids. Taxonomic theorists generally place Thraustochytridswith the algae or algae-like protists. However, because of taxonomicuncertainty, it would be best for the purposes of the present inventionto consider the strains described in the present invention asThraustochytrids to include the following organisms: Order:Thraustochytriales; Family: Thraustochytriaceae (Genera:Thraustochytrium, Schizochytrium, Japonochytrium, Aplanochytrium, orElina) or Labyrinthulaceae (Genera Labyrinthula, Labyrinthuloides, orLabyrinthomyxa). Also, the following genera are sometimes included ineither family Thraustochytriaceae or Labyrinthulaceae: Althornia,Corallochytrium, Diplophyrys, and Pyrrhosorus), and for the purposes ofthis invention are encompassed by reference to a Thraustochytrid or amember of the order Thraustochytriales. It is recognized that at thetime of this invention, revision in the taxonomy of Thraustochytridsplaces the genus Labyrinthuloides in the family of Labyrinthulaceae andconfirms the placement of the two families Thraustochytriaceae andLabyrinthulaceae within the Stramenopile lineage. It is noted that theLabyrinthulaceae are sometimes commonly called labyrinthulids orlabyrinthula, or labyrinthuloides and the Thraustochytriaceae arecommonly called thraustochytrids, although, as discussed above, for thepurposes of clarity of this invention, reference to Thraustochytridsencompasses any member of the order Thraustochytriales and/or includesmembers of both Thraustochytriaceae and Labyrinthulaceae. Recenttaxonomic changes are summarized below.

Strains of certain unicellular microorganisms disclosed herein aremembers of the order Thraustochytriales. Thraustochytrids are marineeukaryotes with an evolving taxonomic history. Problems with thetaxonomic placement of the Thraustochytrids have been reviewed by Moss(in “The Biology of Marine Fungi”, Cambridge University Press p. 105(1986)), Bahnweb and Jackle (ibid. p. 131) and Chamberlain and Moss(BioSystems 21:341 (1988)).

For convenience purposes, the Thraustochytrids were first placed bytaxonomists with other colorless zoosporic eukaryotes in thePhycomycetes (algae-like fungi). The name Phycomycetes, however, waseventually dropped from taxonomic status, and the Thraustochytrids wereretained in the Oomycetes (the biflagellate zoosporic fungi). It wasinitially assumed that the Oomycetes were related to the heterokontalgae, and eventually a wide range of ultrastructural and biochemicalstudies, summarized by Barr (Barr. Biosystems 14:359 (1981)) supportedthis assumption. The Oomycetes were in fact accepted by Leedale(Leedale. Taxon 23:261 (1974)) and other phycologists as part of theheterokont algae. However, as a matter of convenience resulting fromtheir heterotrophic nature, the Oomycetes and Thraustochytrids have beenlargely studied by mycologists (scientists who study fungi) rather thanphycologists (scientists who study algae).

From another taxonomic perspective, evolutionary biologists havedeveloped two general schools of thought as to how eukaryotes evolved.One theory proposes an exogenous origin of membrane-bound organellesthrough a series of endosymbioses (Margulis, 1970, Origin of EukaryoticCells. Yale University Press, New Haven); e.g., mitochondria werederived from bacterial endosymbionts, chloroplasts from cyanophytes, andflagella from spirochaetes. The other theory suggests a gradualevolution of the membrane-bound organelles from the non-membrane-boundedsystems of the prokaryote ancestor via an autogenous process(Cavalier-Smith, 1975, Nature (Lond.) 256:462-468). Both groups ofevolutionary biologists however, have removed the Oomycetes andThraustochytrids from the fungi and place them either with thechromophyte algae in the kingdom Chromophyta (Cavalier-Smith BioSystems14:461 (1981)) (this kingdom has been more recently expanded to includeother protists and members of this kingdom are now called Stramenopiles)or with all algae in the kingdom Protoctista (Margulis and Sagen.Biosystems 18:141 (1985)).

With the development of electron microscopy, studies on theultrastructure of the zoospores of two genera of Thraustochytrids,Thraustochytrium and Schizochytrium, (Perkins, 1976, pp. 279-312 in“Recent Advances in Aquatic Mycology” (ed. E. B. G. Jones), John Wiley &Sons, New York; Kazama. Can. J. Bot. 58:2434 (1980); Barr, 1981,Biosystems 14:359-370) have provided good evidence that theThraustochytriaceae are only distantly related to the Oomycetes.Additionally, genetic data representing a correspondence analysis (aform of multivariate statistics) of 5-S ribosomal RNA sequences indicatethat Thraustochytriales are clearly a unique group of eukaryotes,completely separate from the fungi, and most closely related to the redand brown algae, and to members of the Oomycetes (Mannella et al. Mol.Evol. 24:228 (1987)). Most taxonomists have agreed to remove theThraustochytrids from the Oomycetes (Bartnicki-Garcia. p. 389 in“Evolutionary Biology of the Fungi” (eds. Rayner, A. D. M., Brasier, C.M. & Moore, D.), Cambridge University Press, Cambridge).

In summary, employing the taxonomic system of Cavalier-Smith(Cavalier-Smith. BioSystems 14:461 (1981); Cavalier-Smith. MicrobiolRev. 57:953 (1993)), the Thraustochytrids are classified with thechromophyte algae in the kingdom Chromophyta (Stramenopiles). Thistaxonomic placement has been more recently reaffirmed by Cavalier-Smithet al. using the 18s rRNA signatures of the Heterokonta to demonstratethat Thraustochytrids are chromists not Fungi (Cavalier-Smith et al.Phil. Tran. Roy. Soc. London Series BioSciences 346:387 (1994)). Thisplaces the Thraustochytrids in a completely different kingdom from thefungi, which are all placed in the kingdom Eufungi.

Currently, there are 71 distinct groups of eukaryotic organisms(Patterson. Am. Nat. 154:S96(1999)) and within these groups four majorlineages have been identified with some confidence: (1) Alveolates, (2)Stramenopiles, (3) a Land Plant-green algae-Rhodophyte_Glaucophyte(“plant”) clade and (4) an Opisthokont clade (Fungi and Animals).Formerly these four major lineages would have been labeled Kingdoms butuse of the “kingdom” concept is no longer considered useful by someresearchers.

As noted by Armstrong, Stramenopile refers to three-parted tubularhairs, and most members of this lineage have flagella bearing suchhairs. Motile cells of the Stramenopiles (unicellular organisms, sperm,zoospores) are asymmetrical having two laterally inserted flagella, onelong, bearing three-parted tubular hairs that reverse the thrust of theflagellum, and one short and smooth. Formerly, when the group was lessbroad, the Stramenopiles were called Kingdom Chromista or the heterokont(=different flagella) algae because those groups consisted of the BrownAlgae or Phaeophytes, along with the yellow-green Algae, Golden-brownAlgae, Eustigmatophytes and Diatoms. Subsequently some heterotrophic,fungal-like organisms, the water molds, and labyrinthulids (slime netamoebas), were found to possess similar motile cells, so a group namereferring to photosynthetic pigments or algae became inappropriate.Currently, two of the families within the Stramenopile lineage are theLabyrinthulaceae and the Thraustochytriaceae. Historically, there havebeen numerous classification strategies for these unique microorganismsand they are often classified under the same order (i.e.,Thraustochytriales). Relationships of the members in these groups arestill developing. Porter and Leander have developed data based on 18Ssmall subunit ribosomal DNA indicating the thraustochytrid-labyrinthulidclade in monophyletic. However, the clade is supported by two branches;the first contains three species of Thraustochytrium and Ulkeniaprofunda, and the second includes three species of Labyrinthula, twospecies of Labyrinthuloides and Schizochytrium aggregatum.

The taxonomic placement of the Thraustochytrids as used in the presentinvention is therefore summarized below:

Kingdom: Chromophyta (Stramenopiles)

Phylum: Heterokonta

Order: Thraustochytriales (Thraustochytrids)

Family: Thraustochytriaceae or Labyrinthulaceae

Genera: Thraustochytrium, Schizochytrium, Japonochytrium,Aplanochytrium, Elina, Labyrinthula, Labyrinthuloides, orLabyrinthulomyxa

Some early taxonomists separated a few original members of the genusThraustochytrium (those with an amoeboid life stage) into a separategenus called Ulkenia. However it is now known that most, if not all,Thraustochytrids (including Thraustochytrium and Schizochytrium),exhibit amoeboid stages and as such, Ulkenia is not considered by someto be a valid genus. As used herein, the genus Thraustochytrium willinclude Ulkenia.

Despite the uncertainty of taxonomic placement within higherclassifications of Phylum and Kingdom, the Thraustochytrids remain adistinctive and characteristic grouping whose members remainclassifiable within the order Thraustochytriales.

Another embodiment of the present invention relates to a geneticallymodified plant, wherein the plant has been genetically modified torecombinantly express a PKS system comprising at least one biologicallyactive domain or protein of a polyunsaturated fatty acid (PUFA)polyketide synthase (PKS) system as described herein. The domain of thePUFA PKS system can include any of the domains, including homologuesthereof, for PUFA PKS systems as described above (e.g., for Shewanellajaponica and/or Shewanella olleyana), and can also include any domain ofa PUFA PKS system from any bacterial or non-bacterial microorganism(including any eukaryotic microorganism and any Thraustochytridmicroorganism, such as Schizochytrium and/or Thraustochytrium) or anydomain of a PUFA PKS system from a microorganism identified by ascreening method as described in U.S. patent application Ser. No.10/124,800, supra. The plant can also be further modified with at leastone domain or biologically active fragment thereof of another PKSsystem, including, but not limited to, Type I PKS systems (iterative ormodular), Type II PKS systems, and/or Type III PKS systems. Themodification of the plant can involve the modification and/orutilization of at least one domain of a PUFA PKS system (including aportion of a domain), more than one or several domains of a PUFA PKSsystem (including adjacent domains, non-contiguous domains, or domainson different proteins in the PUFA PKS system), entire proteins of thePUFA PKS system, and the entire PUFA PKS system (e.g., all of theproteins encoded by the PUFA PKS genes) or even more than one PUFA PKSsystem (e.g., one from an organism that naturally produces DHA and onefrom an organism that naturally produces EPA).

As used herein, a genetically modified plant can include any geneticallymodified plant including higher plants and particularly, any consumableplants or plants useful for producing a desired bioactive molecule ofthe present invention. “Plant parts”, as used herein, include any partsof a plant, including, but not limited to, seeds, pollen, embryos,flowers, fruits, shoots, leaves, roots, stems, explants, etc. Agenetically modified plant has a genome which is modified (i.e., mutatedor changed) from its normal (i.e., wild-type or naturally occurring)form such that the desired result is achieved (i.e., increased ormodified PUFA PKS activity and/or production of a desired product usingthe PKS system). Genetic modification of a plant can be accomplishedusing classical strain development and/or molecular genetic techniques.Methods for producing a transgenic plant, wherein a recombinant nucleicacid molecule encoding a desired amino acid sequence is incorporatedinto the genome of the plant, are known in the art. A preferred plant togenetically modify according to the present invention is preferably aplant suitable for consumption by animals, including humans.

Preferred plants to genetically modify according to the presentinvention (i.e., plant host cells) include, but are not limited to anyhigher plants, including both dicotyledonous and monocotyledonousplants, and particularly consumable plants, including crop plants andespecially plants used for their oils. Such plants can include, forexample: canola, soybeans, rapeseed, linseed, corn, safflowers,sunflowers and tobacco. Other preferred plants include those plants thatare known to produce compounds used as pharmaceutical agents, flavoringagents, nutraceutical agents, functional food ingredients orcosmetically active agents or plants that are genetically engineered toproduce these compounds/agents.

According to the present invention, a genetically modified microorganismor plant includes a microorganism or plant that has been modified usingrecombinant technology or by classical mutagenesis and screeningtechniques. As used herein, genetic modifications that result in adecrease in gene expression, in the function of the gene, or in thefunction of the gene product (i.e., the protein encoded by the gene) canbe referred to as inactivation (complete or partial), deletion,interruption, blockage or down-regulation of a gene. For example, agenetic modification in a gene which results in a decrease in thefunction of the protein encoded by such gene, can be the result of acomplete deletion of the gene (i.e., the gene does not exist, andtherefore the protein does not exist), a mutation in the gene whichresults in incomplete or no translation of the protein (e.g., theprotein is not expressed), or a mutation in the gene which decreases orabolishes the natural function of the protein (e.g., a protein isexpressed which has decreased or no enzymatic activity or action).Genetic modifications that result in an increase in gene expression orfunction can be referred to as amplification, overproduction,overexpression, activation, enhancement, addition, or up-regulation of agene.

The genetic modification of a microorganism or plant according to thepresent invention preferably affects the activity of the PKS systemexpressed by the microorganism or plant, whether the PKS system isendogenous and genetically modified, endogenous with the introduction ofrecombinant nucleic acid molecules into the organism (with the option ofmodifying the endogenous system or not), or provided completely byrecombinant technology. To alter the PUFA production profile of a PUFAPKS system or organism expressing such system includes causing anydetectable or measurable change in the production of any one or morePUFAs (or other bioactive molecule produced by the PUFA PKS system) bythe host microorganism or plant as compared to in the absence of thegenetic modification (i.e., as compared to the unmodified, wild-typemicroorganism or plant or the microorganism or plant that is unmodifiedat least with respect to PUFA synthesis—i.e., the organism might haveother modifications not related to PUFA synthesis). To affect theactivity of a PKS system includes any genetic modification that causesany detectable or measurable change or modification in the PKS systemexpressed by the organism as compared to in the absence of the geneticmodification. A detectable change or modification in the PKS system caninclude, but is not limited to: a change or modification (introductionof, increase or decrease) of the expression and/or biological activityof any one or more of the domains in a modified PUFA PKS system ascompared to the endogenous PUFA PKS system in the absence of geneticmodification; the introduction of PKS system activity (i.e., theorganism did not contain a PKS system or a PUFA PKS system prior to thegenetic modification) into an organism such that the organism now hasmeasurable/detectable PKS system activity, such as production of aproduct of a PUFA PKS system; the introduction into the organism of afunctional domain from a different PKS system than the PKS systemendogenously expressed by the organism such that the PKS system activityis modified (e.g., a bacterial PUFA PKS domain as described herein isintroduced into an organism that endogenously expresses a non-bacterialPUFA PKS system, such as a Thraustochytrid); a change in the amount of abioactive molecule (e.g., a PUFA) produced by the PKS system (e.g., thesystem produces more (increased amount) or less (decreased amount) of agiven product as compared to in the absence of the geneticmodification); a change in the type of a bioactive molecule (e.g., achange in the type of PUFA) produced by the PKS system (e.g., the systemproduces an additional or different PUFA, a new or different product, ora variant of a PUFA or other product that is naturally produced by thesystem); and/or a change in the ratio of multiple bioactive moleculesproduced by the PKS system (e.g., the system produces a different ratioof one PUFA to another PUFA, produces a completely different lipidprofile as compared to in the absence of the genetic modification, orplaces various PUFAs in different positions in a triacylglycerol ascompared to the natural configuration). Such a genetic modificationincludes any type of genetic modification and specifically includesmodifications made by recombinant technology and/or by classicalmutagenesis.

It should be noted that reference to increasing the activity of afunctional domain or protein in a PUFA PKS system refers to any geneticmodification in the organism containing the domain or protein (or intowhich the domain or protein is to be introduced) which results inincreased functionality of the domain or protein system and can includehigher activity of the domain or protein (e.g., specific activity or invivo enzymatic activity), reduced inhibition or degradation of thedomain or protein system, and overexpression of the domain or protein.For example, gene copy number can be increased, expression levels can beincreased by use of a promoter that gives higher levels of expressionthan that of the native promoter, or a gene can be altered by geneticengineering or classical mutagenesis to increase the activity of thedomain or protein encoded by the gene.

Similarly, reference to decreasing the activity of a functional domainor protein in a PUFA PKS system refers to any genetic modification inthe organism containing such domain or protein (or into which the domainor protein is to be introduced) which results in decreased functionalityof the domain or protein and includes decreased activity of the domainor protein, increased inhibition or degradation of the domain or proteinand a reduction or elimination of expression of the domain or protein.For example, the action of domain or protein of the present inventioncan be decreased by blocking or reducing the production of the domain orprotein, “knocking out” the gene or portion thereof encoding the domainor protein, reducing domain or protein activity, or inhibiting theactivity of the domain or protein. Blocking or reducing the productionof a domain or protein can include placing the gene encoding the domainor protein under the control of a promoter that requires the presence ofan inducing compound in the growth medium. By establishing conditionssuch that the inducer becomes depleted from the medium, the expressionof the gene encoding the domain or protein (and therefore, of proteinsynthesis) could be turned off. The present inventors demonstrate theability to delete (knock out) targeted genes in a Thraustochytridmicroorganism in the Examples section. Blocking or reducing the activityof domain or protein could also include using an excision technologyapproach similar to that described in U.S. Pat. No. 4,743,546,incorporated herein by reference. To use this approach, the geneencoding the protein of interest is cloned between specific geneticsequences that allow specific, controlled excision of the gene from thegenome. Excision could be prompted by, for example, a shift in thecultivation temperature of the culture, as in U.S. Pat. No. 4,743,546,or by some other physical or nutritional signal.

In one embodiment of the present invention, the endogenous PUFA PKSsystem of a microorganism is genetically modified by, for example,classical mutagenesis and selection techniques and/or molecular genetictechniques, include genetic engineering techniques. Genetic engineeringtechniques can include, for example, using a targeting recombinantvector to delete a portion of an endogenous gene (demonstrated in theExamples) or to replace a portion of an endogenous gene with aheterologous sequence (demonstrated in the Examples). Examples ofheterologous sequences that could be introduced into a host genomeinclude sequences encoding at least one functional PUFA PKS domain orprotein from another PKS system or even an entire PUFA PKS system (e.g.,all genes associated with the PUFA PKS system). A heterologous sequencecan also include a sequence encoding a modified functional domain (ahomologue) of a natural domain from a PUFA PKS system. Otherheterologous sequences that can be introduced into the host genomeinclude a sequence encoding a protein or functional domain that is not adomain of a PKS system per se, but which will affect the activity of theendogenous PKS system. For example, one could introduce into the hostgenome a nucleic acid molecule encoding a phosphopantetheinyltransferase. Specific modifications that could be made to an endogenousPUFA PKS system are discussed in detail herein.

With regard to the production of genetically modified plants, methodsfor the genetic engineering of plants are also well known in the art.For instance, numerous methods for plant transformation have beendeveloped, including biological and physical transformation protocols.See, for example, Miki et al., “Procedures for Introducing Foreign DNAinto Plants” in Methods in Plant Molecular Biology and Biotechnology,Glick, B. R. and Thompson, J. E. Eds. (CRC Press, Inc., Boca Raton,1993) pp. 67-88. In addition, vectors and in vitro culture methods forplant cell or tissue transformation and regeneration of plants areavailable. See, for example, Gruber et al., “Vectors for PlantTransformation” in Methods in Plant Molecular Biology and Biotechnology,Glick, B. R. and Thompson, J. E. Eds. (CRC Press, Inc., Boca Raton,1993) pp. 89-119.

The most widely utilized method for introducing an expression vectorinto plants is based on the natural transformation system ofAgrobacterium. See, for example, Horsch et al., Science 227:1229 (1985).A. tumefaciens and A. rhizogenes are plant pathogenic soil bacteriawhich genetically transform plant cells. The Ti and Ri plasmids of A.tumefaciens and A. rhizogenes, respectively, carry genes responsible forgenetic transformation of the plant. See, for example, Kado, C. I.,Crit. Rev. Plant. Sci. 10:1 (1991). Descriptions of Agrobacterium vectorsystems and methods for Agrobacterium-mediated gene transfer areprovided by numerous references, including Gruber et al., supra, Miki etal., supra, Moloney et al., Plant Cell Reports 8:238 (1989), and U.S.Pat. Nos. 4,940,838 and 5,464,763.

Another generally applicable method of plant transformation ismicroprojectile-mediated transformation wherein DNA is carried on thesurface of microprojectiles. The expression vector is introduced intoplant tissues with a biolistic device that accelerates themicroprojectiles to speeds sufficient to penetrate plant cell walls andmembranes. Sanford et al., Part. Sci. Technol. 5:27 (1987), Sanford, J.C., Trends Biotech. 6:299 (1988), Sanford, J. C., Physiol. Plant 79:206(1990), Klein et al., Biotechnology 10:268 (1992).

Another method for physical delivery of DNA to plants is sonication oftarget cells. Zhang et al., Bio/Technology 9:996 (1991). Alternatively,liposome or spheroplast fusion have been used to introduce expressionvectors into plants. Deshayes et al., EMBO J., 4:2731 (1985), Christouet al., Proc Natl. Acad. Sci. USA 84:3962 (1987). Direct uptake of DNAinto protoplasts using CaCl₂ precipitation, polyvinyl alcohol orpoly-L-ornithine have also been reported. Hain et al., Mol. Gen. Genet.199:161 (1985) and Draper et al., Plant Cell Physiol. 23:451 (1982).Electroporation of protoplasts and whole cells and tissues have alsobeen described. Donn et al., In Abstracts of VIIth InternationalCongress on Plant Cell and Tissue Culture IAPTC, A2-38, p. 53 (1990);D'Halluin et al., Plant Cell 4:1495-1505 (1992) and Spencer et al.,Plant Mol. Biol. 24:51-61 (1994).

In one aspect of this embodiment of the invention, the geneticmodification of an organism (microorganism or plant) can include: (1)the introduction into the host of a recombinant nucleic acid moleculeencoding an amino acid sequence having a biological activity of at leastone domain of a PUFA PKS system; and/or (2) the introduction into thehost of a recombinant nucleic acid molecule encoding at least oneprotein or functional domain that affects the activity of a PUFA PKSsystem. The host can include: (1) a host cell that does not express anyPKS system, wherein all functional domains of a PKS system areintroduced into the host cell, and wherein at least one functionaldomain is from a PUFA PKS system as described herein; (2) a host cellthat expresses a PKS system (endogenous or recombinant) having at leastone functional domain of a PUFA PKS system described herein; and (3) ahost cell that expresses a PKS system (endogenous or recombinant) whichdoes not necessarily include a domain function from a PUFA PKS systemdescribed herein (in this case, the recombinant nucleic acid moleculeintroduced to the host cell includes a nucleic acid sequence encoding atleast one functional domain of the PUFA PKS system described herein). Inother words, the present invention intends to encompass any geneticallymodified organism (e.g., microorganism or plant), wherein the organismcomprises (either endogenously or introduced by recombinantmodification) at least one domain from a PUFA PKS system describedherein (e.g., from or derived from Shewanella japonica or Shewanellaolleyana), wherein the genetic modification has a measurable effect onthe PUFA PKS activity in the host cell.

The present invention relates particularly to the use of PUFA PKSsystems and portions thereof from the marine bacteria described hereinto genetically modify microorganisms and plants to affect the productionof PUFA PKS products by the microorganisms and plants. As discussedabove, the bacteria that are useful in the embodiments of the presentinvention can grow at, and have PUFA PKS systems that are capable ofproducing PUFAs at (e.g., enzymes and proteins that function well at),temperatures approximating or exceeding about 20° C., preferablyapproximating or exceeding about 25° C. and even more preferablyapproximating or exceeding about 30° C. (or any temperature between 20°C. and 30° C. or higher, in whole degree increments, e.g., 21° C., 22°C., 23° C. . . . ). In a preferred embodiment, such bacteria producePUFAs at such temperatures. As described previously herein, the marinebacteria, other Shewanella sp. (e.g., strain SCRC2738) and Vibriomarinus, described in U.S. Pat. No. 6,140,486, do not produce PUFAs (orproduce substantially less or no detectable PUFAs) and do not grow well,if at all, at higher temperatures (e.g., temperatures at or above 20°C.), which limits the usefulness of PUFA PKS systems derived from thesebacteria, particularly in plant applications under field conditions.

In one embodiment of the present invention, one can identify additionalbacteria that have a PUFA PKS system and the ability to grow and producePUFAs at high temperatures. For example, inhibitors of eukaryotic growthsuch as nystatin (antifungal) or cycloheximide (inhibitor of eukaryoticprotein synthesis) can be added to agar plates used to culture/selectinitial strains from water samples/soil samples collected from the typesof habitats/niches such as marine or estuarian habits, or any otherhabitat where such bacteria can be found. This process would help selectfor enrichment of bacterial strains without (or minimal) contaminationof eukaryotic strains. This selection process, in combination withculturing the plates at elevated temperatures (e.g. 20-30° C. or 25-30°C.), and then selecting strains that produce at least one PUFA wouldinitially identify candidate bacterial strains with a PUFA PKS systemthat is operative at elevated temperatures (as opposed to thosebacterial strains in the prior art which only exhibit PUFA production attemperatures less than about 20° C. and more preferably below about 5°C.). To evaluate PUFA PKS function at higher temperatures for genes fromany bacterial source, one can produce cell-free extracts and test forPUFA production at various temperatures, followed by selection ofmicroorganisms that contain PUFA PKS genes that haveenzymatic/biological activity at higher temperature ranges (e.g., 15°C., 20° C., 25° C., or 30° C. or even higher). The present inventorshave identified two exemplary bacteria (e.g. Shewanella olleyana andShewanella japonica; see Examples) that are particularly suitable assources of PUFA PKS genes, and others can be readily identified or areknown to comprise PUFA PKS genes and may be useful in an embodiment ofthe present invention (e.g., Shewanella gelidimarina).

Using the PUFA PKS systems from the particular marine bacteria describedherein, as well as previously described non-bacterial PUFA PKS systemsthat, for example, make use of PUFA PKS genes from Thraustochytrid andother eukaryotic PUFA PKS systems, gene mixing can be used to extend therange of PUFA products to include EPA, DHA, ARA, GLA, SDA and others(described in detail below), as well as to produce a wide variety ofbioactive molecules, including antibiotics, other pharmaceuticalcompounds, and other desirable products. The method to obtain thesebioactive molecules includes not only the mixing of genes from variousorganisms but also various methods of genetically modifying the PUFA PKSgenes disclosed herein. Knowledge of the genetic basis and domainstructure of the bacterial PUFA PKS system of the present inventionprovides a basis for designing novel genetically modified organismswhich produce a variety of bioactive molecules. In particular, the useof the bacterial PUFA PKS genes described herein extends that ability toproduce modified PUFA PKS systems that function and produce high levelsof product at higher temperatures than would be possible using the PUFAPKS genes from previously described marine bacteria. Although mixing andmodification of any PKS domains and related genes are contemplated bythe present inventors, by way of example, various possible manipulationsof the PUFA-PKS system are discussed below with regard to geneticmodification and bioactive molecule production.

Particularly useful PUFA PKS genes and proteins to use in conjunctionwith the marine bacterial PUFA PKS genes described above include thePUFA PKS genes from Thraustochytrids, such as those that have beenidentified in Schizochytrium and Thraustochytrium. Such genes areespecially useful for modification, targeting, introduction into a hostcell and/or otherwise for the gene mixing and modification discussedabove, in combination with various genes, portions thereof andhomologues thereof from the marine bacterial genes described herein.These are described in detail in U.S. patent application Ser. No.10/810,352, supra (Thraustochytrium), in U.S. patent application Ser.No. 10/124,800, supra (Schizochytrium), and in U.S. Pat. No. 6,566,583,supra (Schizochytrium). The PUFA PKS genes in both Schizochytrium andThraustochytrium are organized into three multi-domain-encoding openreading frames, referred to herein as OrfA, OrfB and OrfC.

The complete nucleotide sequence for Schizochytrium OrfA is representedherein as SEQ ID NO:13. OrfA is a 8730 nucleotide sequence (notincluding the stop codon) which encodes a 2910 amino acid sequence,represented herein as SEQ ID NO:14. Within OrfA are twelve domains: (a)one β-ketoacyl-ACP synthase (KS) domain (represented by about position 1to about position 500 of SEQ ID NO:14); (b) one malonyl-CoA:ACPacyltransferase (MAT) domain (represented by about position 575 to aboutposition 1000 of SEQ ID NO:14); (c) nine acyl carrier protein (ACP)domains (represented by about position 1095 to about 2096 of SEQ IDNO:14; and the locations of the active site serine residues (i.e., thepantetheine binding site) for each of the nine ACP domains, with respectto the amino acid sequence of SEQ ID NO:14, are as follows: ACP1=S₁₁₅₇;ACP2=S₁₂₆₆; ACP3=S₁₃₇₇; ACP4=S₁₄₈₈; ACP5=S₁₆₀₄; ACP6=S₁₇₁₅; ACP7=S₁₈₁₉;ACP8=S₁₉₃₀; and ACP9=S₂₀₃₄); and (d) one β-ketoacyl-ACP reductase (KR)domain (represented by about position 2200 to about position 2910 of SEQID NO:14).

The complete nucleotide sequence for Schizochytrium OrfB is representedherein as SEQ ID NO:15. OrfB is a 6177 nucleotide sequence (notincluding the stop codon) which encodes a 2059 amino acid sequence,represented herein as SEQ ID NO:16. Within OrfB are four domains: (a)one β-ketoacyl-ACP synthase (KS) domain (represented by about position 1to about position 450 of SEQ ID NO:16); (b) one chain length factor(CLF) domain (represented by about position 460 to about position 900 ofSEQ ID NO:16); (c) one acyltransferase (AT) domain (represented by aboutposition 901 to about position 1400 of SEQ ID NO:16); and, (d) oneenoyl-ACP reductase (ER) domain (represented by about position 1550 toabout position 2059 of SEQ ID NO:16).

The complete nucleotide sequence for Schizochytrium OrfC is representedherein as SEQ ID NO:17. OrfC is a 4509 nucleotide sequence (notincluding the stop codon) which encodes a 1503 amino acid sequence,represented herein as SEQ ID NO:18. Within OrfC are three domains: (a)two FabA-like β-hydroxyacyl-ACP dehydrase (DH) domains (represented byabout position 1 to about position 450 of SEQ ID NO:18; and representedby about position 451 to about position 950 of SEQ ID NO:18); and (b)one enoyl-ACP reductase (ER) domain (represented by about position 1000to about position 1502 of SEQ ID NO:18).

The complete nucleotide sequence for Thraustochytrium OrfA isrepresented herein as SEQ ID NO:19. OrfA is a 8433 nucleotide sequence(not including the stop codon) which encodes a 2811 amino acid sequence,represented herein as SEQ ID NO:20. Within OrfA are 11 domains: (a) oneβ-ketoacyl-ACP synthase (KS) domain (represented by about position 1 toabout position 500 of SEQ ID NO:20); (b) one malonyl-CoA:ACPacyltransferase (MAT) domain (represented by about position 501 to aboutposition 1000 of SEQ ID NO:20); (c) eight acyl carrier protein (ACP)domains (represented by about position 1069 to about 1998 of SEQ IDNO:20; and the locations of the active site serine residues (i.e., thepantetheine binding site) for each of the nine ACP domains, with respectto the amino acid sequence of SEQ ID NO:20, are as follows: 1128 (ACP1),1244 (ACP2), 1360 (ACP3), 1476 (ACP4), 1592 (ACP5), 1708 (ACP6), 1824(ACP7) and 1940 (ACP8)); and (d) one β-ketoacyl-ACP reductase (KR)domain (represented by about position 2001 to about position 2811 of SEQID NO:20).

The complete nucleotide sequence for Thraustochytrium OrfB isrepresented herein as SEQ ID NO:21. OrfB is a 5805 nucleotide sequence(not including the stop codon) which encodes a 1935 amino acid sequence,represented herein as SEQ ID NO:22. Within OrfB are four domains: (a)one β-ketoacyl-ACP synthase (KS) domain (represented by about position 1to about position 500 of SEQ ID NO:22); (b) one chain length factor(CLF) domain (represented by about position 501 to about position 1000of SEQ ID NO:22); (c) one acyltransferase (AT) domain (represented byabout position 1001 to about position 1500 of SEQ ID NO:22); and, (d)one enoyl-ACP reductase (ER) domain (represented by about position 1501to about position 1935 of SEQ ID NO:22).

The complete nucleotide sequence for Thraustochytrium OrfC isrepresented herein as SEQ ID NO:23. OrfC is a 4410 nucleotide sequence(not including the stop codon) which encodes a 1470 amino acid sequence,represented herein as SEQ ID NO:24. Within Orfc are three domains: (a)two FabA-like β-hydroxyacyl-ACP dehydrase (DH) domains (represented byabout position 1 to about position 500 of SEQ ID NO:24; and representedby about position 501 to about position 1000 of SEQ ID NO:24); and (b)one enoyl-ACP reductase (ER) domain (represented by about position 1001to about position 1470 of SEQ ID NO:24).

Accordingly, encompassed by the present invention are methods togenetically modify microbial or plant cells by: genetically modifying atleast one nucleic acid sequence in the organism that encodes at leastone functional domain or protein (or biologically active fragment orhomologue thereof) of a bacterial PUFA PKS system described herein(e.g., from or derived from the Shewanella japonica or Shewanellaolleyana PUFA PKS systems described herein), and/or expressing at leastone recombinant nucleic acid molecule comprising a nucleic acid sequenceencoding such domain or protein. Various embodiments of such sequences,methods to genetically modify an organism, and specific modificationshave been described in detail above. Typically, the method is used toproduce a particular genetically modified organism that produces aparticular bioactive molecule or molecules.

A particularly preferred embodiment of the present invention relates toa genetically modified plant or part of a plant, wherein the plant hasbeen genetically modified using the PUFA PKS genes described herein sothat the plant produces a desired product of a PUFA PKS system (e.g., aPUFA or other bioactive molecule). Knowledge of the genetic basis anddomain structure of the bacterial PUFA PKS system of the presentinvention combined with the knowledge of the genetic basis and domainstructure for various Thraustochytrid PUFA PKS systems provides a basisfor designing novel genetically modified plants which produce a varietyof bioactive molecules. For example, one can now design and engineer anovel PUFA PKS construct derived from various combinations of domainsfrom the PUFA PKS systems described herein. Such constructs can first beprepared in microorganisms such as E. coli, a yeast, or aThraustochytrid, in order to demonstrate the production of the desiredbioactive molecule, for example, followed by isolation of the constructand use of the same to transform plants to impart similar bioactivemolecule production properties onto the plants. Plants are not known toendogenously contain a PUFA PKS system, and therefore, the PUFA PKSsystems of the present invention represent an opportunity to produceplants with unique fatty acid production capabilities. It is aparticularly preferred embodiment of the present invention togenetically engineer plants to produce one or more PUFAs in the sameplant, including, EPA, DHA, DPA, ARA, GLA, SDA and others. The presentinvention offers the ability to create any one of a number of “designeroils” in various ratios and forms. Moreover, the disclosure of the PUFAPKS genes from the particular marine bacteria described herein offer theopportunity to more readily extend the range of PUFA production andsuccessfully produce such PUFAs within temperature ranges used to growmost crop plants.

Another embodiment of the present invention relates to a geneticallymodified Thraustochytrid microorganism, wherein the microorganism has anendogenous polyunsaturated fatty acid (PUFA) polyketide synthase (PKS)system, and wherein the endogenous PUFA PKS system has been geneticallymodified to alter the expression profile of a polyunsaturated fatty acid(PUFA) by the microorganism as compared to the Thraustochytridmicroorganism in the absence of the modification. Thraustochytridmicroorganisms useful as host organisms in the present inventionendogenously contain and express a PUFA PKS system. The geneticmodification based on the present invention includes the introductioninto the Thraustochytrid of at least one recombinant nucleic acidsequence encoding a PUFA PKS domain or protein (or homologue orfunctional fragment thereof) from a bacterial PUFA PKS system describedherein. The Thraustochytrid may also contain genetic modificationswithin its endogenous PUFA PKS genes, including substitutions,additions, deletions, mutations, and including a partial or completedeletion of the Thraustochytrid PUFA PKS genes and replacement with thePUFA PKS genes from the preferred marine bacteria of the presentinvention.

This embodiment of the invention is particularly useful for theproduction of commercially valuable lipids enriched in a desired PUFA,such as EPA, via the present inventors' development of geneticallymodified microorganisms and methods for efficiently producing lipids(triacylglycerols (TAG) as well as membrane-associated phospholipids(PL)) enriched in PUFAs. Such microorganisms are also useful as“surrogate” hosts to determine optimum gene combinations for later usein the transformation of plant cells, although other microorganisms,including many bacterial and yeast hosts, for example, can also be usedas “surrogate” hosts

This particular embodiment of the present invention is derived in partfrom the following knowledge: (1) utilization of the inherent TAGproduction capabilities of selected microorganisms, and particularly, ofThraustochytrids, such as the commercially developed Schizochytriumstrain ATCC 20888; (2) the present inventors' detailed understanding ofPUFA PKS biosynthetic pathways (i.e., PUFA PKS systems) in eukaryotesand in particular, in members of the order Thraustochytriales, and inthe marine bacteria used in the present invention; and, (3) utilizationof a homologous genetic recombination system in Schizochytrium. Based onthe inventors' knowledge of the systems involved, the same generalapproach may be exploited to produce PUFAs other than EPA.

For example, in one embodiment of the invention, the endogenousThraustochytrid PUFA PKS genes, such as the Schizochytrium genesencoding PUFA PKS enzymes that normally produce DHA and DPA, aremodified by random or targeted mutagenesis, replaced with genes fromother organisms that encode homologous PKS proteins (e.g., from bacteriaor other sources), such as the marine bacterial PUFA PKS genes fromShewanella japonica or Shewanella olleyana described in detail herein,and/or replaced with genetically modified Schizochytrium,Thraustochytrium or other Thraustochytrid PUFA PKS genes. As discussedabove, combinations of nucleic acid molecules encoding various domainsfrom the marine bacterial and Thraustochytrid or other PKS systems canbe “mixed and matched” to create a construct(s) that will result inproduction of a desired PUFA or other bioactive molecule. The product ofthe enzymes encoded by these introduced and/or modified genes can beEPA, for example, or it could be some other related molecule, includingother PUFAs. One feature of this method is the utilization of endogenouscomponents of Thraustochytrid PUFA synthesis and accumulation machinerythat is essential for efficient production and incorporation of the PUFAinto PL and TAG, while taking further advantage of the ability of themarine bacterial genes, for example, to produce EPA. In particular, thisembodiment of the invention is directed to the modification of the typeof PUFA produced by the organism, while retaining the high oilproductivity of the parent strain.

Although some of the following discussion uses the organismSchizochytrium as an exemplary host organism, any Thraustochytrid can bemodified according to the present invention, including members of thegenera Thraustochytrium, Labyrinthuloides, and Japonochytrium. Forexample, Thraustochytrium as described above can also serve as a hostorganism for genetic modification using the methods described herein,although it is more likely that the Thraustochytrium PUFA PKS genes willbe used to modify the endogenous PUFA PKS genes of anotherThraustochytrid, such as Schizochytrium. Furthermore, using methods forscreening organisms as set forth in U.S. application Ser. No.10/124,800, supra, one can identify other organisms useful in thepresent method and all such organisms are encompassed herein. Moreover,PUFA PKS systems can be constructed using the exemplary informationprovided herein, produced in other microorganisms, such as bacteria oryeast, and transformed into plants cells to produce genetically modifiedplants. The concepts discussed herein can be applied to various systemsas desired.

This embodiment of the present invention can be illustrated as follows.By way of example, based on the present inventors' current understandingof PUFA synthesis and accumulation in Schizochytrium, the overallbiochemical process can be divided into three parts.

First, the PUFAs that accumulate in Schizochytrium oil (DHA and DPA) arethe product of a PUFA PKS system as discussed above. The PUFA PKS systemin Schizochytrium converts malonyl-CoA into the end product PUFA withoutrelease of significant amounts of intermediate compounds. InSchizochytrium and also in Thraustochytrium, three genes have previouslybeen identified (Orfs A, B and C; also represented by SEQ ID NOs:13, 15and 17 in Schizochytrium and by SEQ ID NOs:19, 21 and 23 inThraustochytrium, respectively) that encode all of the enzymatic domainsknown to be required for actual synthesis of PUFAs in these organisms.Similar sets of genes (encoding proteins containing homologous sets ofenzymatic domains) have been cloned and characterized from several othernon-eukaryotic organisms that produce PUFAs, namely, several strains ofmarine bacteria, and now in the present invention, the present inventorshave identified and sequenced PUFA PKS genes in two particularly usefulstrains of marine bacteria, Shewanella japonica and Shewanella olleyana.The PUFA products of these marine bacteria are EPA. It is an embodimentof the invention that any PUFA PKS gene set or combinations thereofcould be envisioned to substitute for the Schizochytrium genes describedin the example herein, as long as the physiological growth requirementsof the production organism (e.g., Schizochytrium) in fermentationconditions were satisfied. In particular, the PUFA-producing bacterialstrains described above grow well at relatively high temperatures (e.g.,greater than 25° C.) which further indicates that their PUFA PKS geneproducts will function at standard growth temperatures forSchizochytrium (25-30° C.). It will be apparent to those skilled in theart from this disclosure that other currently unstudied or unidentifiedPUFA-producing bacteria could also contain PUFA PKS genes useful formodification of Thraustochytrids.

Second, in addition to the genes that encode the enzymes directlyinvolved in PUFA synthesis, an “accessory” enzyme is required. The geneencodes a phosphopantetheine transferase (PPTase) that activates theacyl-carrier protein (ACP) domains present in the PUFA PKS complex.Activation of the ACP domains by addition of this co-factor is requiredfor the PUFA PKS enzyme complex to function. All of the ACP domains ofthe PUFA PKS systems identified so far show a high degree of amino acidsequence conservation and, without being bound by theory, the presentinventors believe that the PPTase of Schizochytrium and otherThraustochytrids will recognize and activate ACP domains from other PUFAPKS systems, and vice versa. This gene is identified and included aspart of the PUFA PKS system in the marine bacterial PUFA PKS systemsdescribed herein and can be used in the genetic modification scenariosencompassed by the invention. As proof of principle that heterologousPPTases and PUFA PKS genes can function together to produce a PUFAproduct, the present inventors have demonstrated the use of twodifferent heterologous PPTases with the PUFA PKS genes fromSchizochytrium to produce a PUFA in a bacterial host cell.

Third, in Schizochytrium and other Thraustochytrids, the products of thePUFA PKS system are efficiently channeled into both the phospholipids(PL) and triacylglycerols (TAG). The present inventors' data suggestthat the PUFA is transferred from the ACP domains of the PKS complex tocoenzyme A (CoA). As in other eukaryotic organisms, this acyl-CoA wouldthen serve as the substrate for the various acyl-transferases that formthe PL and TAG molecules. In contrast, the data indicate that inbacteria, transfer to CoA does not occur; rather, there is a directtransfer from the ACP domains of the PKS complex to theacyl-transferases that form PL. The enzymatic system in Schizochytriumthat transfers PUFA from ACP to CoA clearly can recognize both DHA andDPA and therefore, the present inventors believe that it is predictablethat any PUFA product of the PUFA PKS system (as attached to the PUFAPKS ACP domains) will serve as a substrate.

Therefore, in one embodiment of the present invention, the presentinventors propose to alter the genes encoding the components of the PUFAPKS enzyme complex in a Thraustochytrid host (e.g., by introducing atleast one recombinant nucleic acid molecule encoding at least one domainor functional portion thereof from a marine bacteria PUFA PKS of thepresent invention) while utilizing the endogenous PPTase fromSchizochytrium, another Thraustochytrid host, or the PPTase from themarine bacteria of the invention; and PUFA-ACP to PUFA-CoA transferaseactivity and TAG/PL synthesis systems (or other endogenous PUFA ACP toTAG/PL mechanism. These methods of the present invention are supportedby experimental data, some of which are presented in the Examplessection in detail.

The present inventors and others have previously shown that the PUFA PKSsystem can be transferred between organisms, and that some parts areinterchangeable. More particularly, it has been previously shown thatthe PUFA PKS pathways of the marine bacteria, Shewanella SCR2738 (YazawaLipids 31:S297 (1996)) and Vibrio marinus (along with the PPTase fromShewanella) (U.S. Pat. No. 6,140,486), can be successfully transferredto a heterologous host (i.e., to E. coli). Additionally, the degree ofstructural homology between the subunits of the PUFA PKS enzymes fromthese two organisms (Shewanella SCRC2738 and Vibrio marinus) is suchthat it has been possible to mix and match genes from the two systems(U.S. Pat. No. 6,140,486, supra). The functional domains of all of thePUFA PKS enzymes identified so far show some sequence homology to oneanother. Similarly, these data indicated that PUFA PKS systems,including those from the marine bacteria, can be transferred to, andwill function in, Schizochytrium and other Thraustochytrids.

The present inventors have now expressed the PUFA PKS genes (Orfs A, Band C) from Schizochytrium in an E. coli host and have demonstrated thatthe cells made DHA and DPA in about the same ratio as the endogenousproduction of these PUFAs in Schizochytrium (see Example 3). Therefore,it has been demonstrated that the recombinant Schizochytrium PUFA PKSgenes encode a functional PUFA synthesis system. Additionally, all orportions of the Thraustochytrium 23B OrfA and OrfC genes have been shownto function in Schizochytrium (see Example 7). Furthermore, the presentinventors have also replaced the entire Schizochytrium orfC codingsequence completely and exactly by the Thraustochytrium 23B orfC codingsequence, which resulted in a PUFA production profile in theSchizochytrium host that was shifted toward that of Thraustochytrium(see Example 8).

The present inventors have previously found that PPTases can activateheterologous PUFA PKS ACP domains. Production of DHA in E. colitransformed with the PUFA PKS genes from Vibrio marinus occurred onlywhen an appropriate PPTase gene (in this case, from Shewanella SCRC2738)was also present (see U.S. Pat. No. 6,140,486, supra). This demonstratedthat the Shewanella PPTase was able to activate the Vibrio PUFA PKS ACPdomains. Additionally, the present inventors have now demonstrated theactivation (pantetheinylation) of ACP domains from Schizochytrium Orf Ausing a PPTase (sfp) from Bacillus subtilus (see Example 3). The presentinventors have also demonstrated activation (pantetheinylation) of ACPdomains from Schizochytrium Orf A by a PPTase called Het I from Nostoc(see Example 3). The HetI enzyme was additionally used as the PPTase inthe experiments discussed above for the production of DHA and DPA in E.coli using the recombinant Schizochytrium PUFA PKS genes (Example 3).

The data also indicate that DHA-CoA and DPA-CoA may be metabolicintermediates in the Schizochytrium TAG and PL synthesis pathway.Published biochemical data suggest that in bacteria, the newlysynthesized PUFAs are transferred directly from the PUFA PKS ACP domainsto the phospholipid synthesis enzymes. In contrast, the presentinventors' data indicate that in Schizochytrium, a eukaryotic organism,there may be an intermediate between the PUFA on the PUFA PKS ACPdomains and the target TAG and PL molecules. The typical carrier offatty acids in the eukaryotic cytoplasm is CoA. The inventors examinedextracts of Schizochytrium cells and found significant levels ofcompounds that co-migrated during HPLC fractionation with authenticstandards of DHA-CoA, DPA-CoA, 16:0-CoA and 18:1-CoA. The identity ofthe putative DHA-CoA and DPA-CoA peaks were confirmed using massspectroscopy. In contrast, the inventors were not able to detect DHA-CoAin extracts of Vibrio marinus, again suggesting that a differentmechanism exists in bacteria for transfer of the PUFA to its finaltarget (e.g., direct transfer to PL). The data indicate a mechanismlikely exists in Schizochytrium for transfer of the newly synthesizedPUFA to CoA (probably via a direct transfer from the ACP to CoA). BothTAG and PL synthesis enzymes could then access this PUFA-CoA. Theobservation that both DHA and DPA CoA are produced suggests that theenzymatic transfer machinery may recognize a range of PUFAs.

The present inventors have also created knockouts of Orf A, Orf B, andOrf C in Schizochytrium (see Example 4). The knockout strategy relies onthe homologous recombination that has been demonstrated to occur inSchizochytrium (see U.S. patent application Ser. No. 10/124,807, supra).Several strategies can be employed in the design of knockout constructs.The specific strategy used to inactivate these three genes utilizedinsertion of a Zeocin™ resistance gene coupled to a tubulin promoter(derived from pMON50000, see U.S. patent application Ser. No.10/124,807) into a cloned portion of the Orf. The new constructcontaining the interrupted coding region was then used for thetransformation of wild type Schizochytrium cells via particlebombardment (see U.S. patent application Ser. No. 10/124,807). Bombardedcells were spread on plates containing both Zeocin™ and a supply of PUFA(see below). Colonies that grew on these plates were then streaked ontoZeocin™ plates that were not supplemented with PUFAs. Those coloniesthat required PUFA supplementation for growth were candidates for havinghad the PUFA PKS Orf inactivated via homologous recombination. In allthree cases, this presumption was confirmed by rescuing the knockout bytransforming the cells with a full-length genomic DNA clones of therespective Schizochytrium Orfs. Furthermore, in some cases, it was foundthat in the rescued transformants the Zeocin™ resistance gene had beenremoved (see Example 6), indicating that the introduced functional genehad integrated into the original site by double homologous recombination(i.e. deleting the resistance marker). One key to the success of thisstrategy was supplementation of the growth medium with PUFAs. In thepresent case, an effective means of supplementation was found to besequestration of the PUFA by mixing with partially methylatedbeta-cyclodextrin prior to adding to the growth medium (see Example 6).Together, these experiments demonstrate the principle that one of skillin the art, given the guidance provided herein, can inactivate one ormore of the PUFA PKS genes in a PUFA PKS-containing microorganism suchas Schizochytrium, and create a PUFA auxotroph which can then be usedfor further genetic modification (e.g., by introducing other PKS genes)according to the present invention (e.g., to alter the fatty acidprofile of the recombinant organism).

One element of the genetic modification of the organisms of the presentinvention is the ability to directly transform a Thraustochytrid genome.In U.S. application Ser. No. 10/124,807, supra, transformation ofSchizochytrium via single crossover homologous recombination andtargeted gene replacement via double crossover homologous recombinationwere demonstrated. As discussed above, the present inventors have nowused this technique for homologous recombination to inactivate Orf A,Orf B and OrfC of the PUFA-PKA system in Schizochytrium. The resultingmutants are dependent on supplementation of the media with PUFA. Severalmarkers of transformation, promoter elements for high level expressionof introduced genes and methods for delivery of exogenous geneticmaterial have been developed and are available. Therefore, the tools arein place for knocking out endogenous PUFA PKS genes in Thraustochytridsand other eukaryotes having similar PUFA PKS systems and replacing themwith genes from other organisms, such as the marine bacterial genesdescribed herein and as proposed above.

In one approach for production of EPA-rich TAG, the PUFA PKS system ofSchizochytrium can be altered by the addition of heterologous genesencoding a PUFA PKS system whose product is EPA, such as the genes fromShewanella japonica and Shewanella olleyana described herein. It isanticipated that the endogenous PPTase will activate the ACP domains ofthat heterologous PUFA PKS system, but the inventors have also clonedand sequenced the PPTase from the marine bacteria, which could also beintroduced into the host. Additionally, it is anticipated that the EPAwill be converted to EPA-CoA and will readily be incorporated intoSchizochytrium TAG and PL membranes. Therefore, in one embodiment, genesencoding a heterologous PUFA PKS system that produce EPA (e.g., from themarine bacteria above) can be introduced into a microorganism thatnaturally produces DHA (e.g., Schizochytrium) so that the resultingmicroorganism produces both EPA and DHA. This technology can be furtherapplied to genetically modified plants, for example, by introducing thetwo different PUFA PKS systems described above into plant cells toproduce a plant that produces both EPA and DHA, or whatever combinationof PUFAs is desired.

In one modification of this approach, techniques can be used to modifythe relevant domains of the endogenous Schizochytrium system (either byintroduction of specific regions of heterologous genes or by mutagenesisof the Schizochytrium genes themselves) such that its end product is EPArather than DHA and DPA, or alternatively, so that the endproduct isboth EPA and DHA and/or DPA, or so that the endproduct is EPA and ARAinstead of DHA and DPA. This is an exemplary approach, as thistechnology can be applied to the production of other PUFA end productsand to any eukaryotic microorganism that comprises a PUFA PKS system andthat has the ability to efficiently channel the products of the PUFA PKSsystem into both the phospholipids (PL) and triacylglycerols (TAG). Inparticular, the invention is applicable to any Thraustochytridmicroorganism or any other eukaryote that has an endogenous PUFA PKSsystem, which is described in detail below by way of example. Inaddition, the invention is applicable to any suitable host organism,into which the modified genetic material for production of various PUFAprofiles as described herein can be transformed. For example, in theExamples, the PUFA PKS system from Schizochytrium is transformed into anE. coli. Such a transformed organism could then be further modified toalter the PUFA production profile using the methods described herein.

The present invention particularly makes use can make use of genes andnucleic acid sequences which encode proteins or domains from PKS systemsother than the PUFA PKS system described herein and in priorapplications and includes genes and nucleic acid sequences frombacterial and non-bacterial PKS systems, including PKS systems of Type I(iterative or modular), Type II or Type III, described above. Organismswhich express each of these types of PKS systems are known in the artand can serve as sources for nucleic acids useful in the geneticmodification process of the present invention.

In a preferred embodiment, genes and nucleic acid sequences which encodeproteins or domains from PKS systems other than the PUFA PKS system orfrom other PUFA PKS systems are isolated or derived from organisms whichhave preferred growth characteristics for production of PUFAs. Inparticular, it is desirable to be able to culture the geneticallymodified Thraustochytrid microorganism at temperatures at or greaterthan about 15° C., at or greater than 20° C., at or greater than 25° C.,or at or greater than 30° C., or up to about 35° C., or in oneembodiment, at any temperature between about 20° C. and 35° C., in wholedegree increments. Therefore, PKS proteins or domains having functionalenzymatic activity at these temperatures are preferred. The PUFA PKSgenes from Shewanella olleyana or Shewanella japonica described hereinnaturally produce EPA and grow at temperatures up to 25° C., 30° C., or35° C., which makes them particularly useful for this embodiment of theinvention (see Examples 1-2).

In another preferred embodiment, the genes and nucleic acid sequencesthat encode proteins or domains from a PUFA PKS system that produces onefatty acid profile are used to modify another PUFA PKS system andthereby alter the fatty acid profile of the host. For example,Thraustochytrium 23B (ATCC 20892) is significantly different fromSchizochytrium sp. (ATCC 20888) in its fatty acid profile.Thraustochytrium 23B can have DHA:DPA(n-6) ratios as high as 40:1compared to only 2-3:1 in Schizochytrium (ATCC 20888). Thraustochytrium23B can also have higher levels of C20:5(n-3). However, Schizochytrium(ATCC 20888) is an excellent oil producer as compared toThraustochytrium 23B. Schizochytrium accumulates large quantities oftriacylglycerols rich in DHA and docosapentaenoic acid (DPA; 22:5ω6);e.g., 30% DHA+DPA by dry weight. Therefore, the present inventorsdescribe herein the modification of the Schizochytrium endogenous PUFAPKS system with Thraustochytrium 23B PUFA PKS genes to create agenetically modified Schizochytrium with a DHA:DPA profile more similarto Thraustochytrium 23B (i.e., a “super-DHA-producer” Schizochytrium,wherein the production capabilities of the Schizochytrium combine withthe DHA:DPA ratio of Thraustochytrium). This modification isdemonstrated in Example 8.

Therefore, the present invention makes use of genes from certain marinebacterial and any Thraustochytrid or other eukaryotic PUFA PKS systems,and further utilizes gene mixing to extend and/or alter the range ofPUFA products to include EPA, DHA, DPA, ARA, GLA, SDA and others. Themethod to obtain these altered PUFA production profiles includes notonly the mixing of genes from various organisms into the ThraustochytridPUFA PKS genes, but also various methods of genetically modifying theendogenous Thraustochytrid PUFA PKS genes disclosed herein. Knowledge ofthe genetic basis and domain structure of the Thraustochytrid PUFA PKSsystem and the marine bacterial PUFA PKS system provides a basis fordesigning novel genetically modified organisms that produce a variety ofPUFA profiles. Novel PUFA PKS constructs prepared in microorganisms suchas a Thraustochytrid can be isolated and used to transform plants toimpart similar PUFA production properties onto the plants.

Any one or more of the endogenous Thraustochytrid PUFA PKS domains canbe altered or replaced according to the present invention (for examplewith a domain from a marine bacterium of the present invention),provided that the modification produces the desired result (i.e.,alteration of the PUFA production profile of the microorganism).Particularly preferred domains to alter or replace include, but are notlimited to, any of the domains corresponding to the domains inSchizochytrium OrfB or OrfC (β-keto acyl-ACP synthase (KS),acyltransferase (AT), FabA-like β-hydroxy acyl-ACP dehydrase (DH), chainlength factor (CLF), enoyl ACP-reductase (ER), an enzyme that catalyzesthe synthesis of trans-2-acyl-ACP, an enzyme that catalyzes thereversible isomerization of trans-2-acyl-ACP to cis-3-acyl-ACP, and anenzyme that catalyzes the elongation of cis-3-acyl-ACP tocis-5-O-keto-acyl-ACP). In one embodiment, preferred domains to alter orreplace include, but are not limited to, β-keto acyl-ACP synthase (KS),FabA-like β-hydroxy acyl-ACP dehydrase (DH), and chain length factor(CLF).

In one aspect of the invention, Thraustochytrid PUFA-PKS PUFA productionis altered by modifying the CLF (chain length factor) domain. Thisdomain is characteristic of Type II (dissociated enzymes) PKS systems.Its amino acid sequence shows homology to KS (keto synthase pairs)domains, but it lacks the active site cysteine. CLF may function todetermine the number of elongation cycles, and hence the chain length,of the end product. In this embodiment of the invention, using thecurrent state of knowledge of FAS and PKS synthesis, a rational strategyfor production of ARA by directed modification of the non-bacterialPUFA-PKS system is provided. There is controversy in the literatureconcerning the function of the CLF in PKS systems (Bisang et al., Nature401:502 (1999); Yi et al., J. Am. Chem. Soc. 125:12708 (2003)) and it isrealized that other domains may be involved in determination of thechain length of the end product. However, it is significant thatSchizochytrium produces both DHA (C22:6, ω-3) and DPA (C22:5, ω-6). Inthe PUFA-PKS system the cis double bonds are introduced during synthesisof the growing carbon chain. Since placement of the ω-3 and ω-6 doublebonds occurs early in the synthesis of the molecules, one would notexpect that they would affect subsequent end-product chain lengthdetermination. Thus, without being bound by theory, the presentinventors believe that introduction of a factor (e.g. CLF) that directssynthesis of C20 units (instead of C22 units) into the SchizochytriumPUFA-PKS system will result in the production of EPA (C20:5, ω-3) andARA (C20:4, ω-6). For example, in heterologous systems, one couldexploit the CLF by directly substituting a CLF from an EPA producingsystem (such as one from Photobacterium, or preferably from amicroorganism with the preferred growth requirements as described below)into the Schizochytrium gene set. The fatty acids of the resultingtransformants can then be analyzed for alterations in profiles toidentify the transformants producing EPA and/or ARA.

By way of example, in this aspect of the invention, one could constructa clone with the CLF of OrfB replaced with a CLF from a C20 PUFA-PKSsystem, such as the marine bacterial systems described in detail herein.A marker gene could be inserted downstream of the coding region. Morespecifically, one can use the homologous recombination system fortransformation of Thraustochytrids as described herein and in detail inU.S. patent application Ser. No. 10/124,807, supra. One can thentransform the wild type Thraustochytrid cells (e.g., Schizochytriumcells), select for the marker phenotype, and then screen for those thathad incorporated the new CLF. Again, one would analyze thesetransformants for any effects on fatty acid profiles to identifytransformants producing EPA and/or ARA. Alternatively, and in somecases, preferably, such screening for the effects of swapped domains canbe carried out in E. coli (as described below) or in other systems suchas, but not limited to, yeast. If some factor other than thoseassociated with the CLF is found to influence the chain length of theend product, a similar strategy could be employed to alter thosefactors. In another embodiment of the invention, an organism is modifiedby introducing both a chain length factor plus a β-ketoacyl-ACP synthase(KS) domain.

In another aspect of the invention, modification or substitution of theβ-hydroxy acyl-ACP dehydrase/keto synthase pairs is contemplated. Duringcis-vaccenic acid (C18:1, Δ11) synthesis in E. coli, creation of the cisdouble bond is believed to depend on a specific DH enzyme, β-hydroxyacyl-ACP dehydrase, the product of the fabA gene. This enzyme removesHOH from a β-keto acyl-ACP and initially produces a trans double bond inthe carbon chain. A subset of DH's, FabA-like, possess cis-transisomerase activity (Heath et al., 1996, supra). A novel aspect ofbacterial and non-bacterial PUFA-PKS systems is the presence of twoFabA-like DH domains. Without being bound by theory, the presentinventors believe that one or both of these DH domains will possesscis-trans isomerase activity (manipulation of the DH domains isdiscussed in greater detail below).

Another aspect of the unsaturated fatty acid synthesis in E. coli is therequirement for a particular KS enzyme, β-ketoacyl-ACP synthase, theproduct of the fabB gene. This is the enzyme that carries outcondensation of a fatty acid, linked to a cysteine residue at the activesite (by a thio-ester bond), with a malonyl-ACP. In the multi-stepreaction, CO₂ is released and the linear chain is extended by twocarbons. It is believed that only this KS can extend a carbon chain thatcontains a double bond. This extension occurs only when the double bondis in the cis configuration; if it is in the trans configuration, thedouble bond is reduced by enoyl-ACP reductase (ER) prior to elongation(Heath et al., 1996, supra). All of the PUFA-PKS systems characterizedso far have two KS domains, one of which shows greater homology to theFabB-like KS of E. coli than the other. Again, without being bound bytheory, the present inventors believe that in PUFA-PKS systems, thespecificities and interactions of the DH (FabA-like) and KS (FabB-like)enzymatic domains determine the number and placement of cis double bondsin the end products. Because the number of 2-carbon elongation reactionsis greater than the number of double bonds present in the PUFA-PKS endproducts, it can be determined that in some extension cycles completereduction occurs. Thus the DH and KS domains can be used as targets foralteration of the DHA/DPA ratio or ratios of other long chain fattyacids. These can be modified and/or evaluated by introduction ofhomologous domains from other systems or by mutagenesis of these genefragments. In one embodiment, the FabA-like DH domain may not require aKS partner domain at all.

In another embodiment, the ER (enoyl-ACP reductase—an enzyme whichreduces the trans-double bond in the fatty acyl-ACP resulting in fullysaturated carbons) domains can be modified or substituted to change thetype of product made by the PKS system. For example, the presentinventors know that Schizochytrium PUFA-PKS system differs from thepreviously described bacterial systems in that it has two (rather thanone) ER domains. Without being bound by theory, the present inventorsbelieve these ER domains can strongly influence the resulting PKSproduction product. The resulting PKS product could be changed byseparately knocking out the individual domains or by modifying theirnucleotide sequence or by substitution of ER domains from otherorganisms, such as the ER domain from the marine bacteria describedherein.

In another aspect of the invention, substitution of one of the DH(FabA-like) domains of the PUFA-PKS system for a DH domain that does notposses isomerization activity is contemplated, potentially creating amolecule with a mix of cis- and trans-double bonds. The current productsof the Schizochytrium PUFA PKS system are DHA and DPA (C22:5 ω6). If onemanipulated the system to produce C20 fatty acids, one would expect theproducts to be EPA and ARA (C20:4 ω6). This could provide a new sourcefor ARA. One could also substitute domains from related PUFA-PKS systemsthat produced a different DHA to DPA ratio—for example by using genesfrom Thraustochytrium 23B (the PUFA PKS system of which is identified inU.S. patent application Ser. No. 10/124,800, supra).

Additionally, in one embodiment, one of the ER domains is altered in theThraustochytrid PUFA PKS system (e.g. by removing or inactivating) toalter the end product profile. Similar strategies could be attempted ina directed manner for each of the distinct domains of the PUFA-PKSproteins using more or less sophisticated approaches. Of course onewould not be limited to the manipulation of single domains. Finally, onecould extend the approach by mixing domains from the PUFA-PKS system andother PKS or FAS systems (e.g., type I, type II, type III) to create anentire range of new PUFA end products.

As an example of how the bacterial PUFA PKS genes described in detailherein can be used to modify PUFA production in Schizochytrium, thefollowing discussion is provided. Again, all of the examples describedherein may be equally applied to the production of other geneticallymodified microorganisms or to the production of genetically modifiedplants. All presently-known examples of PUFA PKS genes from bacteriaexist as four closely linked genes that contain the same domains as inthe three-gene Schizochytrium set. Indeed, the present inventors havedemonstrated that the PUFA PKS genes from Shewanella olleyana andShewanella japonica are found in this tightly clustered arrangement. TheDNA sequences of the bacterial PUFA PKS genes described herein can nowbe used to design vectors for transformation of Schizochytrium strainsdefective in the endogenous PUFA PKS genes (e.g., see Examples 4, 6 and7). Whole bacterial genes (coding sequences) may be used to replacewhole Schizochytrium genes (coding sequences), thus utilizing theSchizochytrium gene expression regions, and the fourth bacterial genemay be targeted to a different location within the genome.Alternatively, individual bacterial PUFA PKS functional domains may be“swapped” or exchanged with the analogous Schizochytrium domains bysimilar techniques of homologous recombination. As yet anotheralternative, bacterial PUFA PKS genes may even be added to PUFA PKSsystems from Thraustochytrids to produce organisms having more than onePUFA synthase activity. It is understood that the sequence of thebacterial PUFA PKS genes or domains may have to be modified toaccommodate details of Schizochytrium codon usage, but this is withinthe ability of those of skill in the art.

It is recognized that many genetic alterations, either random ordirected, which one may introduce into a native (endogenous, natural)PKS system, will result in an inactivation of enzymatic functions.Therefore, in order to test for the effects of genetic manipulation of aThraustochytrid PUFA PKS system in a controlled environment, one couldfirst use a recombinant system in another host, such as E. coli, tomanipulate various aspects of the system and evaluate the results. Forexample, the FabB strain of E. coli is incapable of synthesizingunsaturated fatty acids and requires supplementation of the medium withfatty acids that can substitute for its normal unsaturated fatty acidsin order to grow (see Metz et al. (2001), supra). However, thisrequirement (for supplementation of the medium) can be removed when thestrain is transformed with a functional PUFA-PKS system (i.e. one thatproduces a PUFA product in the E. coli host—see (Metz et al. (2001),supra, FIG. 2A of that publication). The transformed FabB strain nowrequires a functional PUFA-PKS system (to produce the unsaturated fattyacids) for growth without supplementation. The key element in thisexample is that production of a wide range of unsaturated fatty acidwill suffice (even unsaturated fatty acid substitutes such as branchedchain fatty acids). Therefore, in another preferred embodiment of theinvention, one could create a large number of mutations in one or moreof the PUFA PKS genes disclosed herein, and then transform theappropriately modified FabB strain (e.g. create mutations in anexpression construct containing an ER domain and transform a FabB strainhaving the other essential domains on a separate plasmid—or integratedinto the chromosome) and select only for those transformants that growwithout supplementation of the medium (i.e., that still possessed anability to produce a molecule that could complement the FabB defect).The FabA strain of E. coli has a similar phenotype to the FabB strainand could also be used as an alternative strain in the example describedabove.

One test system for genetic modification of a PUFA PKS is exemplified inthe Examples section. Briefly, a host microorganism such as E. coli istransformed with genes encoding a PUFA PKS system including all or aportion of a Thraustochytrid PUFA PKS system (e.g., Orfs A, B and C ofSchizochytrium) and a gene encoding a phosphopantetheinyl transferases(PPTase), which is required for the attachment of a phosphopantetheinecofactor to produce the active, holo-ACP in the PKS system. The genesencoding the PKS system can be genetically engineered to introduce oneor more modifications to the Thraustochytrid PUFA PKS genes and/or tointroduce nucleic acids encoding domains from other PKS systems into theThraustochytrid genes (including genes from non-Thraustochytridmicroorganisms and genes from different Thraustochytrid microorganisms).The PUFA PKS system can be expressed in the E. coli and the PUFAproduction profile measured. In this manner, potential geneticmodifications can be evaluated prior to manipulation of theThraustochytrid PUFA production organism.

The present invention includes the manipulation of endogenous nucleicacid molecules in a Thraustochytrid PUFA PKS system and/or the use ofisolated nucleic acid molecules comprising a nucleic acid sequence froma Shewanella japonica PUFA PKS system, from a Shewanella olleyana PUFAPKS system, and can additionally include a nucleic acid sequence from aThraustochytrid PUFA PKS system, or homologues of any of such nucleicacid sequences. In one aspect, the present invention relates to themodification and/or use of a nucleic acid molecule comprising a nucleicacid sequence encoding a domain from a PUFA PKS system having abiological activity of at least one of the following proteins:malonyl-CoA:ACP acyltransferase (MAT), β-keto acyl-ACP synthase (KS),ketoreductase (KR), acyltransferase (AT), FabA-like β-hydroxy acyl-ACPdehydrase (DH), phosphopantetheine transferase, chain length factor(CLF), acyl carrier protein (ACP), enoyl ACP-reductase (ER), an enzymethat catalyzes the synthesis of trans-2-acyl-ACP, an enzyme thatcatalyzes the reversible isomerization of trans-2-acyl-ACP tocis-3-acyl-ACP, and/or an enzyme that catalyzes the elongation ofcis-3-acyl-ACP to cis-5-O-keto-acyl-ACP. Preferred domains to modify inorder to alter the PUFA production profile of a host Thraustochytridhave been discussed previously herein.

The genetic modification of an organism according to the presentinvention preferably affects the type, amounts, and/or activity of thePUFAs produced by the organism, whether the organism has an endogenousPUFA PKS system that is genetically modified, and/or whether recombinantnucleic acid molecules are introduced into the organism. According tothe present invention, to affect an activity of a PUFA PKS system, suchas to affect the PUFA production profile, includes any geneticmodification in the PUFA PKS system or genes that interact with the PUFAPKS system that causes any detectable or measurable change ormodification in any biological activity the PUFA PKS system expressed bythe organism as compared to in the absence of the genetic modification.According to the present invention, the phrases “PUFA profile”, “PUFAexpression profile” and “PUFA production profile” can be usedinterchangeably and describe the overall profile of PUFAsexpressed/produced by a organism. The PUFA expression profile caninclude the types of PUFAs expressed by the organism, as well as theabsolute and relative amounts of the PUFAs produced. Therefore, a PUFAprofile can be described in terms of the ratios of PUFAs to one anotheras produced by the organism, in terms of the types of PUFAs produced bythe organism, and/or in terms of the types and absolute or relativeamounts of PUFAs produced by the organism.

As discussed above, the host organism can include any prokaryotic oreukaryotic organism with or without an endogenous PUFA PKS system andpreferably is a eukaryotic microorganism with the ability to efficientlychannel the products of the PUFA PKS system into both the phospholipids(PL) and triacylglycerols (TAG). A preferred host microorganism is anymember of the order Thraustochytriales, including the familiesThraustochytriaceae and Labyrinthulaceae. Particularly preferred hostcells of these families have been described above. Preferred host plantcells include plant cells from any crop plant or plant that iscommercially useful.

In one embodiment of the present invention, it is contemplated that agenetic engineering and/or mutagenesis program could be combined with aselective screening process to obtain a Thraustochytrid microorganismwith the PUFA production profile of interest. The mutagenesis methodscould include, but are not limited to: chemical mutagenesis, shufflingof genes, switching regions of the genes encoding specific enzymaticdomains, or mutagenesis restricted to specific regions of those genes,as well as other methods.

For example, high throughput mutagenesis methods could be used toinfluence or optimize production of the desired PUFA profile. Once aneffective model system has been developed, one could modify these genesin a high throughput manner. Utilization of these technologies can beenvisioned on two levels. First, if a sufficiently selective screen forproduction of a product of interest (e.g., EPA) can be devised, it couldbe used to attempt to alter the system to produce this product (e.g., inlieu of, or in concert with, other strategies such as those discussedabove). Additionally, if the strategies outlined above resulted in a setof genes that did produce the PUFA profile of interest, the highthroughput technologies could then be used to optimize the system. Forexample, if the introduced domain only functioned at relatively lowtemperatures, selection methods could be devised to permit removing thatlimitation.

As described above, in one embodiment of the present invention, agenetically modified microorganism or plant includes a microorganism orplant which has an enhanced ability to synthesize desired bioactivemolecules (products) or which has a newly introduced ability tosynthesize specific products (e.g., to synthesize a specificantibiotic). According to the present invention, “an enhanced ability tosynthesize” a product refers to any enhancement, or up-regulation, in apathway related to the synthesis of the product such that themicroorganism or plant produces an increased amount of the product(including any production of a product where there was none before) ascompared to the wild-type microorganism or plant, cultured or grown,under the same conditions. Methods to produce such genetically modifiedorganisms have been described in detail above and indeed, any exemplarymodifications described using any of the PUFA PKS systems can be adaptedfor expression in plants.

One embodiment of the present invention is a method to produce desiredbioactive molecules (also referred to as products or compounds) bygrowing or culturing a genetically modified microorganism or plant ofthe present invention (described in detail above). Such a methodincludes the step of culturing in a fermentation medium or growing in asuitable environment, such as soil, a microorganism or plant,respectively, that has a genetic modification as described previouslyherein and in accordance with the present invention. Preferred hostcells for genetic modification related to the PUFA PKS system of theinvention are described above.

One embodiment of the present invention is a method to produce desiredPUFAs by culturing a genetically modified microorganism of the presentinvention (described in detail above). Such a method includes the stepof culturing in a fermentation medium and under conditions effective toproduce the PUFA(s) a microorganism that has a genetic modification asdescribed previously herein and in accordance with the presentinvention. An appropriate, or effective, medium refers to any medium inwhich a genetically modified microorganism of the present invention,including Thraustochytrids and other microorganisms, when cultured, iscapable of producing the desired PUFA product(s). Such a medium istypically an aqueous medium comprising assimilable carbon, nitrogen andphosphate sources. Such a medium can also include appropriate salts,minerals, metals and other nutrients. Any microorganisms of the presentinvention can be cultured in conventional fermentation bioreactors. Themicroorganisms can be cultured by any fermentation process whichincludes, but is not limited to, batch, fed-batch, cell recycle, andcontinuous fermentation. Preferred growth conditions for Thraustochytridmicroorganisms according to the present invention are well known in theart and are described in detail, for example, in U.S. Pat. No.5,130,242, U.S. Pat. No. 5,340,742, and U.S. Pat. No. 5,698,244, each ofwhich is incorporated herein by reference in its entirety.

In one embodiment, the genetically modified microorganism is cultured ata temperature of at or greater than about 15° C., and in anotherembodiment, at or greater than about 20° C., and in another embodiment,at or greater than about 25° C., and in another embodiment, at orgreater than about 30° C., and in another embodiment, up to about 35° C.or higher, and in another embodiment, at any temperature between about20° C. and 35° C., in whole degree increments.

The desired PUFA(s) and/or other bioactive molecules produced by thegenetically modified microorganism can be recovered from thefermentation medium using conventional separation and purificationtechniques. For example, the fermentation medium can be filtered orcentrifuged to remove microorganisms, cell debris and other particulatematter, and the product can be recovered from the cell-free supernatantby conventional methods, such as, for example, ion exchange,chromatography, extraction, solvent extraction, phase separation,membrane separation, electrodialysis, reverse osmosis, distillation,chemical derivatization and crystallization. Alternatively,microorganisms producing the PUFA(s), or extracts and various fractionsthereof, can be used without removal of the microorganism componentsfrom the product.

Preferably, a genetically modified microorganism of the inventionproduces one or more polyunsaturated fatty acids including, but notlimited to, EPA (C20:5, ω-3), DHA (C22:6, ω-3), DPA (C22:5, ω-6), ARA(C20:4, ω-6), GLA (C18:3, n-6), and SDA (C18:4, n-3)). In one preferredembodiment, a Schizochytrium that, in wild-type form, produces highlevels of DHA and DPA, is genetically modified according to theinvention to produce high levels of EPA. As discussed above, oneadvantage of using genetically modified Thraustochytrid microorganismsto produce PUFAs is that the PUFAs are directly incorporated into boththe phospholipids (PL) and triacylglycerides (TAG).

Preferably, PUFAs are produced in an amount that is greater than about5% of the dry weight of the microorganism, and in one aspect, in anamount that is greater than 6%, and in another aspect, in an amount thatis greater than 7%, and in another aspect, in an amount that is greaterthan 8%, and in another aspect, in an amount that is greater than 9%,and in another aspect, in an amount that is greater than 10%, and so onin whole integer percentages, up to greater than 90% dry weight of themicroorganism (e.g., 15%, 20%, 30%, 40%, 50%, and any percentage inbetween). In the method for production of desired bioactive compounds ofthe present invention, a genetically modified plant is cultured in afermentation medium or grown in a suitable medium such as soil. Anappropriate, or effective, fermentation medium has been discussed indetail above. A suitable growth medium for higher plants includes anygrowth medium for plants, including, but not limited to, soil, sand, anyother particulate media that support root growth (e.g. vermiculite,perlite, etc.) or hydroponic culture, as well as suitable light, waterand nutritional supplements which optimize the growth of the higherplant. The genetically modified plants of the present invention areengineered to produce significant quantities of the desired productthrough the activity of the PKS system that is genetically modifiedaccording to the present invention. The compounds can be recoveredthrough purification processes which extract the compounds from theplant. In a preferred embodiment, the compound is recovered byharvesting the plant. In this embodiment, the plant can be consumed inits natural state or further processed into consumable products.

Many genetic modifications useful for producing bioactive molecules willbe apparent to those of skill in the art, given the present disclosure,and various other modifications have been discussed previously herein.The present invention contemplates any genetic modification related to aPUFA PKS system as described herein which results in the production of adesired bioactive molecule.

Bioactive molecules, according to the present invention, include anymolecules (compounds, products, etc.) that have a biological activity,and that can be produced by a PKS system that comprises at least oneamino acid sequence having a biological activity of at least onefunctional domain of a non-bacterial PUFA PKS system as describedherein. Such bioactive molecules can include, but are not limited to: apolyunsaturated fatty acid (PUFA), an anti-inflammatory formulation, achemotherapeutic agent, an active excipient, an osteoporosis drug, ananti-depressant, an anti-convulsant, an anti-Heliobactor pylori drug, adrug for treatment of neurodegenerative disease, a drug for treatment ofdegenerative liver disease, an antibiotic, and a cholesterol loweringformulation. One advantage of the PUFA PKS system of the presentinvention is the ability of such a system to introduce carbon-carbondouble bonds in the cis configuration, and molecules including a doublebond at every third carbon. This ability can be utilized to produce avariety of compounds.

Preferably, bioactive compounds of interest are produced by thegenetically modified microorganism in an amount that is greater thanabout 0.05%, and preferably greater than about 0.1%, and more preferablygreater than about 0.25%, and more preferably greater than about 0.5%,and more preferably greater than about 0.75%, and more preferablygreater than about 1%, and more preferably greater than about 2.5%, andmore preferably greater than about 5%, and more preferably greater thanabout 10%, and more preferably greater than about 15%, and even morepreferably greater than about 20% of the dry weight of themicroorganism. For lipid compounds, preferably, such compounds areproduced in an amount that is greater than about 5% of the dry weight ofthe microorganism. For other bioactive compounds, such as antibiotics orcompounds that are synthesized in smaller amounts, those strainspossessing such compounds at of the dry weight of the microorganism areidentified as predictably containing a novel PKS system of the typedescribed above. In some embodiments, particular bioactive molecules(compounds) are secreted by the microorganism, rather than accumulating.Therefore, such bioactive molecules are generally recovered from theculture medium and the concentration of molecule produced will varydepending on the microorganism and the size of the culture.

One embodiment of the present invention relates to a method to modify anendproduct so that it contains at least one fatty acid (although theendproduct may already contain at least one fatty acid, whereby at leastone additional fatty acid is provided by the present method), comprisingadding to the endproduct an oil produced by a recombinant host cell(microbial or plant) that expresses at least one recombinant nucleicacid molecule comprising a nucleic acid sequence encoding at least onebiologically active domain of a PUFA PKS system. The PUFA PKS systemincludes any suitable bacterial or non-bacterial PUFA PKS systemdescribed herein, including the bacterial PUFA PKS systems fromShewanella japonica or Shewanella olleyana, or any PUFA PKS system fromother bacteria that normally (i.e., under normal or natural conditions)are capable of growing and producing PUFAs at temperatures above 22° C.

Preferably, the endproduct is selected from the group consisting of afood, a dietary supplement, a pharmaceutical formulation, a humanizedanimal milk, and an infant formula. Suitable pharmaceutical formulationsinclude, but are not limited to, an anti-inflammatory formulation, achemotherapeutic agent, an active excipient, an osteoporosis drug, ananti-depressant, an anti-convulsant, an anti-Heliobactor pylon drug, adrug for treatment of neurodegenerative disease, a drug for treatment ofdegenerative liver disease, an antibiotic, and a cholesterol loweringformulation. In one embodiment, the endproduct is used to treat acondition selected from the group consisting of: chronic inflammation,acute inflammation, gastrointestinal disorder, cancer, cachexia, cardiacrestenosis, neurodegenerative disorder, degenerative disorder of theliver, blood lipid disorder, osteoporosis, osteoarthritis, autoimmunedisease, preeclampsia, preterm birth, age related maculopathy, pulmonarydisorder, and peroxisomal disorder.

Suitable food products include, but are not limited to, fine bakerywares, bread and rolls, breakfast cereals, processed and unprocessedcheese, condiments (ketchup, mayonnaise, etc.), dairy products (milk,yogurt), puddings and gelatin desserts, carbonated drinks, teas,powdered beverage mixes, processed fish products, fruit-based drinks,chewing gum, hard confectionery, frozen dairy products, processed meatproducts, nut and nut-based spreads, pasta, processed poultry products,gravies and sauces, potato chips and other chips or crisps, chocolateand other confectionery, soups and soup mixes, soya based products(milks, drinks, creams, whiteners), vegetable oil-based spreads, andvegetable-based drinks.

Yet another embodiment of the present invention relates to a method toproduce a humanized animal milk. This method includes the steps ofgenetically modifying milk-producing cells of a milk-producing animalwith at least one recombinant nucleic acid molecule comprising a nucleicacid sequence encoding at least one biologically active domain of a PUFAPKS system as described herein.

Methods to genetically modify a host cell and to produce a geneticallymodified non-human, milk-producing animal, are known in the art.Examples of host animals to modify include cattle, sheep, pigs, goats,yaks, etc., which are amenable to genetic manipulation and cloning forrapid expansion of a transgene expressing population. For animals,PKS-like transgenes can be adapted for expression in target organelles,tissues and body fluids through modification of the gene regulatoryregions. Of particular interest is the production of PUFAs in the breastmilk of the host animal.

The following examples are provided for the purpose of illustration andare not intended to limit the scope of the present invention.

EXAMPLES Example 1

The following example shows that certain EPA-producing bacteria containPUFA PKS-like genes that appear to be suitable for modification ofSchizochytrium.

Two EPA-producing marine bacterial strains of the genus Shewanella havebeen shown to grow at temperatures typical of Schizochytriumfermentations and to possess PUFA PKS-like genes. Shewanella olleyana(Australian Collection of Antarctic Microorganisms (ACAM) strain number644; Skerratt et al., Int. J. Syst. Evol. Microbiol 52, 2101 (2002))produces EPA and grows up to 25-30° C. Shewanella japonica (AmericanType Culture Collection (ATCC) strain number BAA-316; Ivanova et al.,Int. J. Syst. Evol. Microbiol. 51, 1027 (2001)) produces EPA and growsup to 30-35° C.

To identify and isolate the PUFA-PKS genes from these bacterial strains,degenerate PCR primer pairs for the KS-MAT region of bacterial orf5/pfaAgenes and the DH-DH region of bacterial orf7/pfaC genes were designedbased on published gene sequences for Shewanella SCRC-2738, Shewanellaoneidensis MR-1; Shewanella sp. GA-22; Photobacter profundum, andMoritella marina (see discussion above). Specifically, the primers andPCR conditions were designed as follows:

Primers for the KS/AT region; based on the following publishedsequences: Shewanella sp. SCRC-2738; Shewanella oneidensis MR-1;Photobacter profundum; Moritella marina: prRZ23 GGYATGMTGRTTGGTGAAGG(forward; SEQ ID NO:25) prRZ24 TRTTSASRTAYTGYGAACCTTG (reverse; SEQ IDNO:26)

Primers for the DH region; based on the following published sequences:Shewanella sp. GA-22; Shewanella sp. SCRC-2738; Photobacter profundum;Moritella marina: prRZ28 ATGKCNGAAGGTTGTGGCCA (forward; SEQ ID NO:27)prRZ29 CCWGARATRAAGCCRTTDGGTTG (reverse; SEQ ID NO:28)The PCR conditions (with bacterial chromosomal DNA as templates) were asfollows:

Reaction Mixture:

0.2 μM dNTPs

0.1 μM each primer

8% DMSO

250 ng chromosomal DNA

2.5 U Herculase® DNA polymerase (Stratagene)

1× Herculase® buffer

50 μL total volume

PCR Protocol: (1) 98° C. for 3 min.; (2) 98° C. for 40 sec.; (3) 56° C.for 30 sec.; (4) 72° C. for 90 sec.; (5) Repeat steps 2-4 for 29 cycles;(6) 72° C. for 10 min.; (7) Hold at 6° C.

For both primer pairs, PCR gave distinct products with expected sizesusing chromosomal DNA templates from either Shewanella olleyana orShewanella japonica. The four respective PCR products were cloned intopCR-BLUNT II-TOPO (Invitrogen) and insert sequences were determinedusing the M13 forward and reverse primers. In all cases, the DNAsequences thus obtained were highly homologous to known bacterial PUFAPKS gene regions.

The DNA sequences obtained from the bacterial PCR products were comparedwith known sequences and with PUFA PKS genes from Schizochytrium ATCC20888 in a standard Blastx search (BLAST parameters: Low Complexityfilter: On; Matrix: BLOSUM62; Word Size: 3; Gap Costs: Existance 11,Extension 1 (BLAST described in Altschul, S. F., Madden, T. L.,Schääffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J.(1997) “Gapped BLAST and PSI-BLAST: a new generation of protein databasesearch programs.” Nucleic Acids Res. 25:3389-3402, incorporated hereinby reference in its entirety)).

At the amino acid level, the sequences with the greatest degree ofhomology to the Shewanella olleyana ACAM644 ketoacyl synthase/acyltransferase (KS-AT) deduced amino acid sequence were: Photobacterprofundum pfaA (identity=70%; positives 81%); Shewanella oneidensis MR-1“multi-domain β-ketoacyl synthase” (identity 66%; positives=77%); andMoritella marina ORF8 (identity=56%; positives 71%). The Schizochytriumsp. ATCC20888 orfA was 41% identical and 56% positive to the deducedamino acid sequence for Shewanella olleyana KS-AT.

At the amino acid level, the sequences with the greatest degree ofhomology to the Shewanella japonica ATCC BAA-316 ketoacyl synthase/acyltransferase (KS-AT) deduced amino acid sequence were: Shewanellaoneidensis MR-1 “multi-domain β-ketoacyl synthase” (identity=67%;positives=79%); Shewanella sp. SCRC-2738 orf5 (identity=69%;positives=77%); and Moritella marina ORF8 (identity=56%; positives=70%).The Schizochytrium sp. ATCC20888 orfA was 41% identical and 55% positiveto the deduced amino acid sequence for Shewanella japonica KS-AT.

At the amino acid level, the sequences with the greatest degree ofhomology to the Shewanella olleyana ACAM644 dehydrogenase (DH) deducedamino acid sequence were: Shewanella sp. SCRC-2738 orf7 (identity=77%;positives=86%); Photobacter profundum pfaC (identity=72%;positives=81%); and Shewanella oneidensis MR-1 “multi-domain β-ketoacylsynthase” (identity=75%; positives=83%). The Schizochytrium sp.ATCC20888 orfC was 26% identical and 42% positive to the deduced aminoacid sequence for Shewanella olleyana DH.

At the amino acid level, the sequences with the greatest degree ofhomology to the Shewanella japonica ATCC BAA-316 dehydrogenase (DH)deduced amino acid

sequence were: Shewanella sp. SCRC-2738 orf7 (identity 77%;positives=86%); Photobacter profundum pfaC (identity=73%; positives 83%)and Shewanella oneidensis MR-1 “multi-domain β-ketoacyl synthase”(identity=74%; positives=81%). The Schizochytrium sp. ATCC20888 orfC was27% identical and 42% positive to the deduced amino acid sequence forShewanella japonica DH.

Example 2

The following example demonstrates the generation, identification,sequencing and analysis of DNA clones encoding the complete PUFA PKSsystems from Shewanella japonica and Shewanella olleyana.

Shewanella japonica and Shewanella olleyana recombinant libraries,consisting of large genomic DNA fragments (approximately 40 kB), weregenerated by standard methods in the cosmid vector Supercos-1(Stratagene). The cosmid libraries were screened by standard colonyhybridization procedures. The Sh. olleyana cosmid library was screenedusing two separate digoxigenin-labeled probes. Each probe contained afragment of DNA homologous to a segment of EPA biosynthetic geneclusters described in Example 1 above and respectively represent bothends of the clusters. These probes were generated by PCR using Sh.olleyana DNA as a template and primers prRZ23 (SEQ ID NO:25) and prRZ24(SEQ ID NO:26) for one probe and prRZ28 (SEQ ID NO:27) and prRZ29 (SEQID NO:28) for a second probe. Example 1 above describes these degenerateprimers and the derived PCR products containing DNA fragments homologousto segments of EPA biosynthetic genes. Sh. japonica specific probes weregenerated in a similar manner and the cosmid library was screened. Inall cases, strong hybridization of the individual probes to certaincosmids indicated clones containing DNA homologous to EPA biosyntheticgene clusters.

Clones with strong hybridization to both probes were then assayed forheterologous production of EPA in E. coli. Cells of individual isolatesof E. coli cosmid clones were grown in 2 mL of LB broth overnight at 30°C. with 200 rpm shaking. 0.5 mL of this subculture was used to inoculate25 mL of LB broth and the cells were grown at 20° C. for 20 hours. Thecells were then harvested via centrifugation and dried bylyophilization. The dried cells were analyzed for fat content and fattyacid profile and content using standard gas chromatography procedures.No EPA was detected in fatty acids prepared from control cells of E.coli containing the empty Supercos-1 vector. E. coli strains containingcertain cosmids from S. japonica and S. olleyana typically producedbetween 3-8% EPA of total fatty acids.

Cosmid 9A10 from Sh. olleyana and cosmid 3F3 from Sh. japonica wereselected for total random sequencing. The cosmid clones were randomlyfragmented and subcloned, and the resulting random clones weresequenced. The chromatograms were analyzed and assembled into contigswith the Phred, Phrap and Consed programs (Ewing, et al., Genome Res.8(3):175-185 (1998); Ewing, et al., Genome Res. 8(3): 186-194 (1998);Gordon et al., Genome Res. 8(3):195-202 (1998)). Each nucleotide basepair of the final contig was covered with at least a minimum aggregatedPhred score of 40 (confidence level 99.995%).

The nucleotide sequence of the 39669 bp contig from cosmid 3F3 is shownas SEQ ID NO:1. The nucleotide sequence of the 38794 bp contig fromcosmid 9A10 is shown as SEQ ID NO:7. The sequences of the variousdomains and proteins for the PUFA PKS gene clusters from Shewanellajaponica (cosmid 3F3) and Shewanella olleyana (cosmid 9A10) aredescribed in detail previously herein, and are represented in SEQ IDNOs:2-6 and 8-12, respectively.

Protein comparisons described herein were performed using standard BLASTanalysis (BLAST parameters: Blastp, low complexity filter On,program—BLOSUM62, Gap cost—Existence: 11, Extension 1; (BLAST describedin Altschul, S. F., Madden, T. L., Schääffer, A. A., Zhang, J., Zhang,Z., Miller, W. & Lipman, D. J. (1997) “Gapped BLAST and PSI-BLAST: a newgeneration of protein database search programs.” Nucleic Acids Res.25:3389-3402)). Domain identification was performed using the ConservedDomain Database and Search Service (CD-Search), v2.01. The CD-Search isa public access program available through the public database for theNational Center for Biotechnology Information, sponsored by the NationalLibrary of Medicine and the National Institutes of Health. The CD-Searchcontains protein domains from various databases. The CD-Search uses aBLAST algorithm to identify domains in a queried protein sequence(Marchler-Bauer A, Bryant S H. “CD-Search: protein domain annotations onthe fly.” Nucleic Acids Res. 32:W327-331 (2004)). Finally, Open ReadingFrame (ORF) identification was aided by the use of the EasyGene 1.0Server (Larsen T S, Krogh A. “EasyGene—a prokaryotic gene finder thatranks ORFs by statistical significance”, BMC Bioinformatics 2003, 4:21)and GeneMark.hmm 2.1 (Lukashin A. and Borodovsky M., “GeneMark.hmm: newsolutions for gene finding” Nucleic Acids Res., Vol. 26, No. 4, pp.1107-1115. 1998). The default settings were used in the EasyGeneanalysis and Vibrio cholerae was used as the reference organism. Thedefault settings were used with the GeneMark.hmm program and thePseudonative.model as the setting for the model organism. These programsuse a Hidden Markov Models algorithms to predict bacterial genes.

Table 1 shows an overview/analysis of ORFs from cosmid 3F3 fromShewanella japonica, including start and stop codon coordinates based onSEQ ID NO:1, total nucleotide length of each ORF, total amino acids foreach predicted protein, calculated molecular weight of each predictedprotein, highest homolog in a BLASTp query against the public GenBankdatabase, GI accession number (“GenInfo Identifier” sequenceidentification number) of the most homologous entry in the GenBankdatabase, and proposed function (if related to EPA production).

Table 2 shows an overview/analysis of ORFs from cosmid 9A10 fromShewanella olleyana, including start and stop codon coordinates based onSEQ ID NO:7, and the same additional information that was presented inTable 1 for Shewanella japonica.

Table 3 shows the percent identity of deduced proteins from EPA clustersof Shewanella japonica (cosmid 3F3) compared to Shewanella olleyana(cosmid 9A10) and also compared to proteins from EPA-producing organismshaving the highest levels of identity in the public sequence database.Table 4 shows the same analysis as Table 3 with regard to nucleotideidentity.

Table 5 shows the 23 nucleotides upstream from all of the annotated pfaORFs with possible ribosome binding sites being underlined, as well asthe alternative start codon and upstream nucleotides for ORFs that areannotated to start with the TTG start codon. TABLE 1 ORF analysis ofcosmid 3F3 from Shewanella japonica Start Stop total nt total AccessionProposed function ORF Codon Codon length AA MW Homology of deducedprotein Number of deduced protein orf1* 1195 548 648 215 24561.35 sydprotein GI: 24373178 Shewanella oneidensis MR-1 orf2 1255 2109 855 28432825.47 conserved hypothetical protein GI: 24373177 Shewanellaoneidensis MR-1 orf3 2196 2834 639 212 23779.30 pseudouridylate synthaseGI: 23123676 Nostoc punctiforme orf4* 3832 2873 960 319 36135.31 LysRtranscriptional regulator GI: 24373176 Shewanella oneidensis MR-1 orf53962 5956 1995 664 73468.40 metallo-beta-lactamase GI: 24373175superfamily protein Shewanella oneidensis MR-1 pfaE* 7061 6150 912 30334678.40 orf2 GI: 2529415 phosphopantetheinyl Shewanella sp. SCRC-2738transferase orf6* 9249 7222 2028 675 73367.16 Translation elongationfactor GI: 27358908 Vibrio vulnificus CMCP6 orf7 9622 10494 873 29032540.64 putative transcriptional regulator GI: 24373172 Shewanellaoneidensis MR-1 pfaA 10491 18854 8364 2787 294907.67 PfaApolyunsaturated fatty GI: 46913082 EPA synthase acid synthasePhotobacterium profundum pfaB 18851 21130 2280 759 82727.25 PfaBpolyunsaturated fatty GI: 46913081 EPA synthase acid synthasePhotobacterium profundum pfaC 21127 27186 6060 2019 219255.74 PfaCpolyunsaturated fatty GI: 15488033 EPA synthase acid synthasePhotobacterium profundum pfaD 27197 28825 1692 542 59116.36 orf8 GI:2529421 EPA synthase Shewanella sp. SCRC-2738 orf8 29445 30926 1482 49356478.03 putative cellulosomal protein GI: 7208813 Clostridiumthermocellum orf9 31105 32712 1608 535 59618.32 methyl-acceptingchemotaxis GI: 24374914 protein Shewanella oneidensis MR-1 orf10 3298833845 858 285 32119.88 Glutathione S-transferase GI: 27359215 Vibriovulnificus CMCP6*on the reverse complementary strand

TABLE 2 ORF analysis of cosmid 9A10 from Shewanella olleyana Start Stoptotal nt total Accession Proposed function ORF Codon Codon length AA MWHomology of deduced protein Number of deduced protein orf1* 4160 3531630 209 23724.40 acetyltransferase, GNAT family GI: 24373183 Shewanellaoneidensis MR-1 orf2* 4992 4606 387 128 14034.86 hypothetical proteinGI: 24373181 Shewanella oneidensis MR-1 orf3 5187 5522 336 111 12178.79hypothetical protein GI: 24373180 Shewanella oneidensis MR-1 orf4 56446417 774 257 29674.73 hypothetical protein GI: 24373179 Shewanellaoneidensis MR-1 orf5* 7148 6495 654 217 24733.33 syd protein GI:24373178 Shewanella oneidensis MR-1 orf6 7208 8062 855 284 32749.29hypothetical protein GI: 24373177 Shewanella oneidensis MR-1 orf7 88418131 711 236 26178.32 putative phosphatase GI: 28899965 Vibrioparahaemolyticus orf8 9167 9808 642 213 23849.14 pseudouridylatesynthase GI: 23123676 Nostoc punctiforme orf9* 10797 9805 993 33037337.29 LysR transcriptional regulator GI: 24373176 Shewanellaoneidensis MR-1 orf10 10968 12962 1995 664 72982.72metallo-beta-lactamase GI: 24373175 superfamily protein Shewanellaoneidensis MR-1 pfaE* 13899 13027 873 290 32864.30 orf2 GI: 2529415phosphopantetheinyl Shewanella sp. SCRC-2738 transferase orf11* 1619514156 2040 679 74070.34 Translation elongation factor GI: 27358908Vibrio vulnificus CMCP6 orf12 16568 17440 873 290 32741.82 putativetranscriptional regulator GI: 24373172 Shewanella oneidensis MR-1 pfaA17437 25743 8307 2768 293577.27 PfaA polyunsaturated fatty GI: 46913082EPA synthase acid synthase Photobacterium profundum pfaB 25740 279712232 743 80446.82 PfaB polyunsaturated fatty GI: 46913081 EPA synthaseacid synthase Photobacterium profundum pfaC 27968 34030 6063 2020218810.57 PfaC polyunsaturated fatty GI: 15488033 EPA synthase acidsynthase Photobacterium profundum pfaD 34041 35669 1629 542 59261.59orf8 GI: 2529421 EPA synthase Shewanella sp. SCRC-2738*on the reverse complementary strand

TABLE 3 Amino Acid Percent Identity Shewanella Shewanella japonica (3F3)olleyana (9A10) PfaA Shewanella japonica (3F3) 87.7 Shewanella olleyana(9A10) 87.7 Shewanella sp. SCRC-2738 Orf5 63 63.4 Photobacteriumprofundum S9 PfaA 60.9 62.2 Moritella marina Orf8 41.6 42.9 PfaBShewanella japonica (3F3) 70.3 Shewanella olleyana (9A10) 70.3Shewanella sp. SCRC-2738 Orf6 39.8 38.4 Photobacterium profundum S9 PfaB39 39.6 Moritella marina Orf9 19 18.4 PfaC Shewanella japonica (3F3)85.7 Shewanella olleyana (9A10) 85.7 Shewanella sp. SCRC-2738 Orf7 65.164.8 Photobacterium profundum S9 PfaC 64.6 64.6 Moritella marina Orf1047.3 47.1 PfaD Shewanella japonica (3F3) 98.2 Shewanella olleyana (9A10)98.2 Shewanella sp. SCRC-2738 Orf8 84.2 84 Photobacterium profundum S9PfaD 93.8 64.6 Moritella marina Orf11 63 62.6 PfaE Shewanella japonica(3F3) 61.2 Shewanella olleyana (9A10) 61.2 Shewanella sp. SCRC-2738 Orf236.7 38 Anabaena sp. PCC 7120 HetI 22.6 24.8 Bacillus subtilis Sfp 20.120.7

TABLE 4 Nucleic Acid Percent Identity Shewanella Shewanella japonica(3F3) olleyana (9A10) pfaA Shewanella japonica (3F3) 83.1 Shewanellaolleyana (9A10) 83.1 Shewanella sp. SCRC-2738 orf5 65.5 65.5Photobacterium profundum S9 pfaA 63.5 64.4 Moritella marina orf8 56 56.2pfaB Shewanella japonica (3F3) 70.4 Shewanella olleyana (9A10) 70.4Shewanella sp. SCRC-2738 orf6 54.7 54.5 Photobacterium profundum S9 pfaB53.4 52.6 Moritella marina orf9 42.2 40.6 pfaC Shewanella japonica (3F3)79.6 Shewanella olleyana (9A10) 79.6 Shewanella sp. SCRC-2738 orf7 66.267.2 Photobacterium profundum S9 pfaC 66 66.7 Moritella marina orf1058.3 58.8 pfaD Shewanella japonica (3F3) 89.5 Shewanella olleyana (9A10)89.5 Shewanella sp. SCRC-2738 orf8 77.4 77.8 Photobacterium profundum S9pfaD 75.9 76.0 Moritella marina orf11 63.5 62.9 pfaE Shewanella japonica(3F3) 65 Shewanella olleyana (9A10) 65 Shewanella sp. SCRC-2738 orf2 4344.4 Anabaena sp. PCC 7120 hetI 43.1 38.6 Bacillus subtilis sfp 34.632.9

TABLE 5 Predicted start sites of ORFs from EPA biosynthesis clusters(start codons shown in bold) Possible ribosome binding sites areunderlined ALL pfa ORFs 3F3 CTGAACACTGGAGACTCAAA ATG pfaA SEQ ID NO:33GCTGACTTGCAGGAGTCTGT GTG pfaB SEQ ID NO:34 CAATTAGAAGGAGAACAATC TTG pfaCSEQ ID NO:35 AGAGGCATAAAGGAATAATA ATG pfaD SEQ ID NO:36GCGACCTAGAACAAGCGACA ATG pfaE SEQ ID NO:37 9A10 CTGAACACTGGAGACTCAAA ATGpfaA SEQ ID NO:38 GCTGATTTGCAGGAGTCTGT GTG pfaB SEQ ID NO:39CAATTAGAAGGAGAACAATC TTG pfaC SEQ ID NO:40 AGAGGCATAAAGGAATAATA ATG pfaDSEQ ID NO:41 CAATTTAGCCTGAGCCTAGT TTG pfaE SEQ ID NO:42 pfaC AlternateStart Comparisons 3F3 CAATTAGAAGGAGAACAATC TTG pfaC TAAATCGCACTGGTATTGTCATG pfaC SEQ ID NO:43 alternate #1 AAGCACTCAATGATGCTGGT GTG pfaC SEQ IDNO:44 alternate #2 pfaC alternate #1 starts at nucleotide 21514 of SEQID NO:1 This is 387 nucleotides downstream of annotated pfaC start pfaCalternate #2 starts at nucleotide 21460 of SEQ ID NO:1 This is 333nucleotides downstream of annotated pfaC start 9A10 CAATTAGAAGGAGAACAATCTTG pfaC TAAACCGCACCGGTATTGTC ATG pfaC SEQ ID NO:45 alternate #1ACCCAGCTGACTATCAAGGT GTG pfaC SEQ ID NO:46 alternate #2 pfaC alternate#1 starts at nucleotide 28370 of SEQ ID NO:7 This is 402 nucleotidesdownstream of annotated pfaC start pfaC alternate #2 starts atnucleotide 28151 of SEQ ID NO:7 This is 183 nucleotides downstream ofannotated pfaC start pfaE Alternate Start Comparisons 9A10CAATTTAGCCTGAGCCTAGT TTG pfaE ATGAATCGACTGCGTCTATT GTG pfaE SEQ ID NO:47alternate #1 CATCTAGAGAACAAGGTTTA ATG pfaE SEQ ID NO:48 alternate #2pfaE alternate #1 starts at nucleotide 13821 of SEQ ID NO:7 This is 78nucleotides upstream of the annotated pfaE startpfaE alternate #2 starts at nucleotide 13743 of SEQ ID NO:7 This is 156nucleotides upstream of the annotated pfaE start

Example 3

The following example demonstrates that Schizochytrium Orfs A, B and Cencode a functional DHA/DPA synthesis enzyme via functional expressionin E. coli.

General Preparation of E. coli Transformants

The three genes encoding the Schizochytrium PUFA PKS system that produceDHA and DPA (Orfs A, B & C; SEQ ID NO:13, SEQ ID NO:15 and SEQ ID NO:17,respectively) were cloned into a single E. coli expression vector(derived from pET21c (Novagen)). The genes are transcribed as a singlemessage (by the T7 RNA-polymerase), and a ribosome-binding site clonedin front of each of the genes initiates translation. Modification of theOrf B coding sequence was needed to obtain production of a full-lengthOrf B protein in E. coli (see below). An accessory gene, encoding aPPTase (see below) was cloned into a second plasmid (derived frompACYC184, New England Biolabs).

The Orf B gene is predicted to encode a protein with a mass of ˜224 kDa.Initial attempts at expression of the gene in E. coli resulted inaccumulation of a protein with an apparent molecular mass of ˜165 kDa(as judged by comparison to proteins of known mass during SDS-PAGE).Examination of the Orf B nucleotide sequence revealed a regioncontaining 15 sequential serine codons—all of them being the TCT codon.The genetic code contains 6 different serine codons, and three of theseare used frequently in E. coli. The present inventors used fouroverlapping oligonucleotides in combination with a polymerase chainreaction protocol to resynthesize a small portion of the Orf B gene (a˜195 base pair, BspHI to SacII restriction enzyme fragment) thatcontained the serine codon repeat region. In the synthetic Orf Bfragment, a random mixture of the 3 serine codons commonly used by E.coli was used, and some other potentially problematic codons werechanged as well (i.e., other codons rarely used by E. coli). The BspHIto SacII fragment present in the original Orf B was replaced by theresynthesized fragment (to yield Orf B*) and the modified gene wascloned into the relevant expression vectors. The modified OrfB* stillencodes the amino acid sequence of SEQ ID NO:16. Expression of themodified Orf B* clone in E. coli resulted in the appearance of a ˜224kDa protein, indicating that the full-length product of OrfB wasproduced. The sequence of the resynthesized Orf B* BspHI to SacIIfragment is represented herein as SEQ ID NO:29. Referring to SEQ IDNO:29, the nucleotide sequence of the resynthesized BspHI to SacIIregion of Orf B is shown. The BspHI restriction site and the SacIIrestriction site are identified. The BspHI site starts at nucleotide4415 of the Orf B CDS (SEQ ID NO:15) (note: there are a total of threeBspHI sites in the Orf B CDS, while the SacII site is unique).

The ACP domains of the Orf A protein (SEQ ID NO:14 in Schizochytrium)must be activated by addition of phosphopantetheine group in order tofunction. The enzymes that catalyze this general type of reaction arecalled phosphopantetheine transferases (PPTases). E. coli contains twoendogenous PPTases, but it was anticipated that they would not recognizethe Orf A ACP domains from Schizochytrium. This was confirmed byexpressing Orfs A, B* (see above) and C in E. coli without an additionalPPTase. In this transformant, no DHA production was detected. Theinventors tested two heterologous PPTases in the E. coli PUFA PKSexpression system: (1) sfp (derived from Bacillus subtilis) and (2) HetI (from the cyanobacterium Nostoc strain 7120).

The sfp PPTase has been well characterized and is widely used due to itsability to recognize a broad range of substrates. Based on publishedsequence information (Nakana, et al., 1992, Molecular and GeneralGenetics 232: 313-321), an expression vector for sfp was built bycloning the coding region, along with defined up- and downstreamflanking DNA sequences, into a pACYC-184 cloning vector. Theoligonucleotides: (forward; SEQ ID NO:30)CGGGGTACCCGGGAGCCGCCTTGGCTTTGT; and (reverse; SEQ ID NO:31)AAACTGCAGCCCGGGTCCAGCTGGCAGGCACCCTG,were used to amplify the region of interest from genomic B. subtilusDNA. Convenient restriction enzyme sites were included in theoligonucleotides to facilitate cloning in an intermediate, high copynumber vector and finally into the EcoRV site of pACYC184 to create theplasmid: pBR301. Examination of extracts of E. coli transformed withthis plasmid revealed the presence of a novel protein with the mobilityexpected for sfp. Co-expression of the sfp construct in cells expressingthe Orf A, B*, C proteins, under certain conditions, resulted in DHAproduction. This experiment demonstrated that sfp was able to activatethe Schizochytrium Orf A ACP domains. In addition, the regulatoryelements associated with the sfp gene were used to create an expressioncassette into which other genes could be inserted. Specifically, the sfpcoding region (along with three nucleotides immediately upstream of theATG) in pBR301 was replaced with a 53 base pair section of DNA designedso that it contains several unique (for this construct) restrictionenzyme sites. The initial restriction enzyme site in this region isNdeI. The ATG sequence embedded in this site is utilized as theinitiation methionine codon for introduced genes. The additionalrestriction sites (BglLL, NotI, SmaI, PmelI, HindIII, SpeI and XhoI)were included to facilitate the cloning process. The functionality ofthis expression vector cassette was tested by using PCR to generate aversion of sfp with a NdeI site at the 5′ end and an XhoI site ate the3′ end. This fragment was cloned into the expression cassette andtransferred into E. coli along with the Orf A, B* and C expressionvector. Under appropriate conditions, these cells accumulated DHA,demonstrating that a functional sfp had been produced.

To the present inventors' knowledge, Het I had not been testedpreviously in a heterologous situation. Het I is present in a cluster ofgenes in Nostoc known to be responsible for the synthesis of long chainhydroxy-fatty acids that are a component of a glyco-lipid layer presentin heterocysts of that organism. The present inventors, without beingbound by theory, believe that Het I activates the ACP domains of aprotein, Hgl E, present in that cluster. The two ACP domains of Hgl Ehave a high degree of sequence homology to the ACP domains found inSchizochytrium Orf A. SEQ ID NO:32 represents the amino acid sequence ofthe Nostoc Het I protein. The endogenous start codon of Het I has notbeen identified (there is no methionine present in the putativeprotein). There are several potential alternative start codons (e.g.,TTG and ATT) near the 5′ end of the open reading frame. No methioninecodons (ATG) are present in the sequence. A Het I expression constructwas made by using PCR to replace the furthest 5′ potential alternativestart codon (TTG) with a methionine codon (ATG, as part of the abovedescribed NdeI restriction enzyme recognition site), and introducing anXhoI site at the 3′ end of the coding sequence. The modified HetI codingsequence was then inserted into the NdeI and XhoI sites of the pACYC184vector construct containing the sfp regulatory elements. Expression ofthis Het I construct in E. coli resulted in the appearance of a newprotein of the size expected from the sequence data. Co-expression ofHet I with Schizochytrium Orfs A, B*, C in E. coli under severalconditions resulted in the accumulation of DHA and DPA in those cells.In all of the experiments in which sfp and Het I were compared, more DHAand DPA accumulated in the cells containing the Het I construct than incells containing the sfp construct.

Production of DHA and DPA in E. coli Transformants

The two plasmids encoding: (1) the Schizochytrium PUFA PKS genes (OrfsA, B* and C) and (2) the PPTase (from sfp or from Het I) weretransformed into E. coli strain BL21 which contains an inducible T7 RNApolymerase gene. Synthesis of the Schizochytrium proteins was induced byaddition of IPTG to the medium, while PPTase expression was controlledby a separate regulatory element (see above). Cells were grown undervarious defined conditions and using either of the two heterologousPPTase genes. The cells were harvested and the fatty acids wereconverted to methyl-esters (FAME) and analyzed using gas-liquidchromatography.

Under several conditions, DHA and DPA were detected in E. coli cellsexpressing the Schizochytrium PUFA PKS genes, plus either of the twoheterologous PPTases (data not shown). No DHA or DPA was detected inFAMEs prepared from control cells (i.e., cells transformed with aplasmid lacking one of the Orfs). The ratio of DHA to DPA observed in E.coli approximates that of the endogenous DHA and DPA production observedin Schizochytrium. The highest level of PUFA (DHA plus DPA),representing 17% of the total FAME, was found in cells grown at 32° C.in 765 medium (recipe available from the American Type CultureCollection) supplemented with 10% (by weight) glycerol. PUFAaccumulation was also observed when cells were grown in Luria Brothsupplemented with 5 or 10% glycerol, and when grown at 20° C. Selectionfor the presence of the respective plasmids was maintained by inclusionof the appropriate antibiotics during the growth, and IPTG (to a finalconcentration of 0.5 mM) was used to induce expression of Orfs A, B* andC.

Example 4

The following example demonstrates that genes encoding theSchizochytrium PUFA PKS enzyme complex can be selectively inactivated(knocked out), and that it is a lethal phenotype unless the medium issupplemented with polyunsaturated fatty acids.

Homologous recombination has been demonstrated in Schizochytrium (seecopending U.S. patent application Ser. No. 10/124,807, incorporatedherein by reference in its entirety). A plasmid designed to inactivateSchizochytrium Orf A (SEQ ID NO:13) was made by inserting a Zeocin™resistance marker into the Sma I site of a clone containing the Orf Acoding sequence. The Zeocin™ resistance marker was obtained from theplasmid pMON50000—expression of the Zeocin™ resistance gene is driven bya Schizochytrium derived tubulin promoter element (see U.S. patentapplication Ser. No. 10/124,807, ibid.). The knock-out construct thusconsists of: 5′ Schizochytrium Orf A coding sequence, the tub-Zeocin™resistance element and 3′ Schizochytrium Orf A coding sequence, allcloned into pBluescript II SK (+) vector (Stratagene).

The plasmid was introduced into Schizochytrium cells by particlebombardment and transformants were selected on plates containing Zeocin™and supplemented with polyunsaturated fatty acids (PUFA) (see Example5). Colonies that grew on the Zeocin™ plus PUFA plates were tested forability to grow on plates without the PUFA supplementation and severalwere found that required the PUFA. These PUFA auxotrophs are putativeOrf A knockouts. Northern blot analysis of RNA extracted from several ofthese mutants confirmed that a full-length Orf A message was notproduced in these mutants.

These experiments demonstrate that a Schizochytrium gene (e.g., Orf A)can be inactivated via homologous recombination, that inactivation ofOrf A results in a lethal phenotype, and that those mutants can berescued by supplementation of the media with PUFA.

Similar sets of experiments directed to the inactivation ofSchizochytrium Orf B (SEQ ID NO:15) and Orf C (SEQ ID NO:17) haveyielded similar results. That is, Orf B and Orf C can be individuallyinactivated by homologous recombination and those cells require PUFAsupplementation for growth.

Example 5

The following example shows that PUFA auxotrophs can be maintained onmedium supplemented with EPA, demonstrating that EPA can substitute forDHA in Schizochytrium.

As indicated in Example 4, Schizochytrium cells in which the PUFA PKScomplex has been inactivated required supplementation with PUFA tosurvive. Aside from demonstrating that Schizochytrium is dependent onthe products of this system for growth, this experimental system permitsthe testing of various fatty acids for their ability to rescue themutants. It was discovered that the mutant cells (in which any of thethree genes have been inactivated) grew as well on media supplementedwith EPA as they did on media supplemented with DHA. This resultindicates that, if the endogenous PUFA PKS complex which produces DHAwere replaced with one whose product was EPA, the cells would be viable.Additionally, these mutant cells could be rescued by supplementationwith either ARA or GLA, demonstrating the feasibility of producinggenetically modified Schizochytrium that produce these products. It isnoted that a preferred method for supplementation with PUFAs involvescombining the free fatty acids with partially methylatedbeta-cyclodextrin prior to addition of the PUFAs to the medium.

Example 6

The following example shows that inactivated PUFA genes can be replacedat the same site with active forms of the genes in order to restore PUFAsynthesis.

Double homologous recombination at the acetolactate synthase gene sitehas been demonstrated in Schizochytrium (see U.S. patent applicationSer. No. 10/124,807, supra). The present inventors tested this conceptfor replacement of the Schizochytrium PUFA PKS genes by transformationof a Schizochytrium Orf A knockout strain (described in Example 3) witha full-length Schizochytrium Orf A genomic clone. The transformants wereselected by their ability to grow on media without supplemental PUFAs.These PUFA prototrophs were then tested for resistance to Zeocin™ andseveral were found that were sensitive to the antibiotic. These resultsindicate that the introduced Schizochytrium Orf A has replaced theZeocin™ resistance gene in the knockout strain via double homologousrecombination. This experiment demonstrates the proof of concept forgene replacement within the PUFA PKS genes. Similar experiments forSchizochytrium Orf B and Orf C knock-outs have given identical results.

Example 7

This example shows that all or some portions of the Thraustochytrium 23BPUFA PKS genes can function in Schizochytrium.

As described in U.S. patent application Ser. No. 10/124,800 (supra), theDHA-producing protist Thraustochytrium 23B (Th. 23B) has been shown tocontain orfA, orfb, and orfC homologs. Complete genomic clones of thethree Th. 23B genes were used to transform the Zeocin™-resistantSchizochytrium strains containing the cognate orf “knock-out” (seeExample 4). Direct selection for complemented transformants was carriedout in the absence of PUFA supplementation. By this method, it was shownthat the Th. 23B orfA and orfC genes could complement the SchizochytriumorfA and orfC knock-out strains, respectively, to PUFA prototrophy.Complemented transformants were found that either retained or lostZeocin™ resistance (the marker inserted into the Schizochytrium genesthereby defining the knock-outs). The Zeocin™-resistant complementedtransformants are likely to have arisen by a single cross-overintegration of the entire Thraustochytrium gene into the Schizochytriumgenome outside of the respective orf region. This result suggests thatthe entire Thraustochytrium gene is functioning in Schizochytrium. TheZeocin™-sensitive complemented transformants are likely to have arisenby double cross-over events in which portions (or conceivably all) ofthe Thraustochytrium genes functionally replaced the cognate regions ofthe Schizochytrium genes that had contained the disruptive Zeocin™resistance marker. This result suggests that a fraction of theThraustochytrium gene is functioning in Schizochytrium.

Example 8

In this example, the entire Schizochytrium orfC coding sequence iscompletely and exactly replaced by the Thraustochytrium 23B orfC codingsequence resulting in a PUFA profile shifted toward that ofThraustochytrium.

To delete the Schizochytrium orfC coding sequence, approximately 2 kb ofDNA immediately upstream (up to but not including the ATG start codon)and immediately downstream (beginning just after the TAA stop codon)were cloned around the Zeocin™ resistance marker. The upstream anddownstream regions provide homology for double crossover recombinationeffectively replacing the orfC coding sequence with the marker.Transformants are selected for Zeocin™ resistance in the presence ofsupplemental PUFA, screened for PUFA auxotrophy, and characterized byPCR and Southern blot analysis. Similarly, a plasmid was constructed inwhich the same upstream and downstream sequences of the SchizochytriumorfC gene region were cloned around the Th. 23B orf C coding sequence(SEQ ID NO:23). Transformation of this plasmid into the Zeocin™resistant PUFA auxotroph described above was carried out with selectionfor PUFA prototrophy, thus relying on the Th. 23B orfC gene to functioncorrectly in Schizochytrium and complement the PUFA auxotrophy.Subsequent screening for Zeocin™ sensitive transformants identifiedthose likely to have arisen from a replacement of the Zeocin™ resistancemarker with the Th. 23B orfC gene. The DHA:DPA ratio in these orfCreplacement strains was on average 8.3 versus a normal (“wild type”)value of 2.3. This higher ratio approximates the value of 10 forThraustochytrium 23B under these growth conditions. Therefore, it isshown that the PUFA profile of Schizochytrium can be manipulated bysubstituting components of the PUFA synthase enzyme complex.

More specifically, the first pair of plasmids captures the regionsimmediately “upstream” and “downstream” of the Schizochytrium orfC geneand was used to construct both the orfC deletion vector as well as theTh. 23B replacement vector.

Primers prRZ15 (SEQ ID NO:49) and prRZ16 (SEQ ID NO:50) were used toamplify a 2000 bp fragment upstream of the orfC coding region from aclone of the Schizochytrium orfC region. Primer prRZ15 incorporates aKpnI site at the 5-prime end of the fragment and prRZ16 containshomology to Schizochytrium sequence up to but not including the ATGstart codon and incorporates a BamHI site at the 3-prime end of thefragment. The PCR product was cloned into pCR-Blunt II (Invitrogen)resulting in plasmid pREZ21. In a similar manner, primers prRZ17 (SEQ IDNO:51) and prRZ18 (SEQ ID NO:52) were used to amplify a 1991 bp fragmentimmediately downstream of the orfC coding region (not containing the TAAstop codon) but incorporating a BamHI site at the 5-prime end and a XbaIsite at the 3-prime end. This PCR fragment was cloned into pCR-Blunt II(Invitrogen) to create pREZ18. In a three-component ligation, theupstream region from pREZ21 (as a KpnI-BamHI fragment) and thedownstream region from pREZ18 (as a BamHI-XbaI fragment) were clonedinto the KpnI-XbaI site of pBlueScriptII SK(+) to yield pREZ22. TheZeocin™ resistance marker from pTUBZEO11-2 (a.k.a. pMON50000; see U.S.patent application Ser. No. 10/124,807, supra) as an 1122 bp BamHIfragment was inserted into the BamHI site of pREZ22 to produce pREZ23Aand pREZ23B (containing the Zeocin™ resistance marker in eitherorientation). The pREZ23 plasmids were then used to create the precisedeletion of the orfC coding region by particle bombardmenttransformation as described above. A strain with the desired structureis named B32-Z1.

To develop the plasmid for insertion of the Th. 23B orfC gene,intermediate constructs containing the precise junctions between 1) theSchizochytrium upstream region and the 5-prime end of the Th. 23B orfCcoding region and 2) the 3-prime end of the Th. 23B orfC coding regionand the Schizochytrium downstream region are first produced. Then, theinternal section of the Th. 23B orfC coding region is introduced.

Primers prRZ29a (SEQ ID NO:53) and prRZ30 (SEQ ID NO:54) are used toamplify approximately 100 bp immediately upstream of the SchizochytriumorfC coding sequence. Primer prRZ29a includes the SpeI restriction siteapproximately 95 bp upstream of the Schizochytrium orfC ATG start codon,and prRZ30 contains homology to 19 bp immediately upstream of theSchizochytrium orfC ATG start codon and 15 bp homologous to the start ofthe Th. 23B orfC coding region (including the start ATG). Separately, anapproximately 450 bp PCR product is generated from the 5-prime end ofthe Th. 23B orfC coding region using the cloned Th. 23B gene as atemplate. Primer prRZ31 contains 15 bp of the Schizochytrium orfC codingsequence immediately upstream of the start ATG and homology to 17 bp atthe start of the Th. 23B orfC coding region, and primer prRZ32incorporates the NruI site located at approximately 450 bp downstream ofthe Th. 23B orfC ATG start codon and further includes an artificial SwaIrestriction site just downstream of the NruI site. These two PCRproducts therefore have about 30 bp of overlapping homology with eachother at the start ATG site essentially comprising the sequences ofprRZ30 (SEQ ID NO:54) and prRZ31 (SEQ ID NO:55). A second round of PCRusing a mix of the two first-round PCR products (prRZ29a (SEQ ID NO:53)X prRZ30 (SEQ ID NO:54); ca. 100 bp; prRZ31 (SEQ ID NO:55) X prRZ32 (SEQID NO:56); ca. 450 bp) as template and the outside primers prRZ29a (SEQID NO:53) and prRZ32 (SEQ ID NO:56) resulted in an approximately 520 bpproduct containing the “perfect stitch” between the upstreamSchizochytrium orfC region and the start of the Th. 23B orf C codingregion. This PCR product was cloned into plasmid pCR-Blunt II to createpREZ28, and the sequence of the insert was confirmed.

Primers prRZ33 (SEQ ID NO:57) and prRZ34 (SEQ ID NO:58) were used forPCR to generate a fragment of approximately 65 bp at the 3-prime end ofthe Th. 23B orf C coding region using the cloned Th. 23B gene as atemplate. The upstream end of this fragment (from prRZ33) contains anartificial SwaI restriction site and encompasses the SphI restrictionsite at approximately 60 bp upstream of the Th. 23B orfC TAA terminationcodon. The downstream end of this fragment (from prRZ34) contains 16 bpat the 3-prime end of the Th. 23B orf C coding region and 18 bp withhomology to Schizochytrium sequences immediately downstream from theorfC coding region (including the termination codon). Primers prRZ35(SEQ ID NO:59) and prRZ36 (SEQ ID NO:60) were used to generate afragment of approximately 250 bp homologous to Schizochytrium DNAimmediately downstream of the orfC coding region. The upstream end ofthis PCR fragment (from prRZ35) contained 15 bp homologous to the end ofthe Th. 23B orf C coding region (counting the TAA stop codon), and thedownstream end contained the SalI restriction site about 240 bpdownstream of the Schizochytrium stop codon. A second round of PCR usinga mix of the two first-round PCR products (prRZ33 (SEQ ID NO:57) XprRZ34 (SEQ ID NO:58); ca. 65 bp; prRZ35 (SEQ ID NO:59) X prRZ36 (SEQ IDNO:60); ca. 250 bp) as template and the outside primers prRZ33 (SEQ IDNO:57) and prRZ36 (SEQ ID NO:60) resulted in an approximately 310 bpproduct containing the “perfect stitch” between the end of theThraustochytrium 23B orfC coding region and the region of SchizochytriumDNA immediately downstream of the orfC coding region. This PCR productwas cloned into plasmid pCR-Blunt II to create pREZ29, and the sequenceof the insert was confirmed.

Next, the upstream and downstream “perfect stitch” regions were combinedinto pREZ22 (see above). In a three component ligation, the SpeI/SwaIfragment from pREZ28 and the SwaI/SalI fragment of pREZ29 were clonedinto the SpeI/SalI sites of pREZ22 to create pREZ32. Lastly, theinternal bulk of the Thraustochytrium 23B orfC coding region was clonedinto pREZ32 as a NruI/SphI fragment to create pREZ33. This plasmid wasthen used to transform the orfC knock-out strain B32-Z1 with selectionfor PUFA prototrophy.

Each publication cited or discussed herein is incorporated herein byreference in its entirety.

While various embodiments of the present invention have been describedin detail, it is apparent that modifications and adaptations of thoseembodiments will occur to those skilled in the art. It is to beexpressly understood, however, that such modifications and adaptationsare within the scope of the present invention, as set forth in thefollowing claims.

1-86. (canceled)
 87. An isolated nucleic acid molecule comprising anucleic acid sequence encoding an amino acid sequence that is at least70% identical to amino acid positions 29-513 of SEQ ID NO:8 or that isan enzymatically active fragment of amino acid positions 29-513 of SEQID NO:8, wherein said amino acid sequence has β-ketoacyl-ACP synthase(KS) activity.
 88. The isolated nucleic acid molecule of claim 87,comprising a nucleic acid sequence encoding an amino acid sequence thatis at least 90% identical to amino acid positions 29-513 of SEQ ID NO:8,wherein said amino acid sequence has β-ketoacyl-ACP synthase (KS)activity.
 89. The isolated nucleic acid molecule of claim 87, comprisinga nucleic acid sequence encoding an amino acid sequence that is at least95% identical to amino acid positions 29-513 of SEQ ID NO:8, whereinsaid amino acid sequence has β-ketoacyl-ACP synthase (KS) activity. 90.The isolated nucleic acid molecule of claim 87, consisting of a nucleicacid sequence encoding an amino acid sequence that is at least 95%identical to amino acid positions 29-513 of SEQ ID NO:8, wherein saidamino acid sequence has β-ketoacyl-ACP synthase (KS) activity.
 91. Theisolated nucleic acid molecule of claim 87, comprising a nucleic acidsequence encoding an amino acid sequence that is at least 96% identicalto amino acid positions 29-513 of SEQ ID NO:8, wherein said amino acidsequence has β-ketoacyl-ACP synthase (KS) activity.
 92. The isolatednucleic acid molecule of claim 87, consisting of a nucleic acid sequenceencoding an amino acid sequence that is at least 96% identical to aminoacid positions 29-513 of SEQ ID NO:8, wherein said amino acid sequencehas β-ketoacyl-ACP synthase (KS) activity.
 93. The isolated nucleic acidmolecule of claim 87, comprising a nucleic acid sequence encoding anamino acid sequence that is at least 97% identical to amino acidpositions 29-513 of SEQ ID NO:8, wherein said amino acid sequence hasβ-ketoacyl-ACP synthase (KS) activity.
 94. The isolated nucleic acidmolecule of claim 87, consisting of a nucleic acid sequence encoding anamino acid sequence that is at least 97% identical to amino acidpositions 29-513 of SEQ ID NO:8, wherein said amino acid sequence hasβ-ketoacyl-ACP synthase (KS) activity.
 95. The isolated nucleic acidmolecule of claim 87, comprising a nucleic acid sequence encoding anamino acid sequence that is at least 98% identical to amino acidpositions 29-513 of SEQ ID NO:8, wherein said amino acid sequence hasβ-ketoacyl-ACP synthase (KS) activity.
 96. The isolated nucleic acidmolecule of claim 87, consisting of a nucleic acid sequence encoding anamino acid sequence that is at least 98% identical to amino acidpositions 29-513 of SEQ ID NO:8, wherein said amino acid sequence hasβ-ketoacyl-ACP synthase (KS) activity.
 97. The isolated nucleic acidmolecule of claim 87, comprising a nucleic acid sequence encoding anamino acid sequence that is at least 99% identical to amino acidpositions 29-513 of SEQ ID NO:8, wherein said amino acid sequence hasβ-ketoacyl-ACP synthase (KS) activity.
 98. The isolated nucleic acidmolecule of claim 87, consisting of a nucleic acid sequence encoding anamino acid sequence that is at least 99% identical to amino acidpositions 29-513 of SEQ ID NO:8, wherein said amino acid sequence hasβ-ketoacyl-ACP synthase (KS) activity.
 99. The isolated nucleic acidmolecule of claim 87, comprising a nucleic acid sequence encoding aminoacid positions 29-513 of SEQ ID NO:8.
 100. The isolated nucleic acidmolecule of claim 87, consisting of a nucleic acid sequence encodingamino acid positions 29-513 of SEQ ID NO:8.
 101. The isolated nucleicacid molecule of claim 87, wherein the nucleic acid molecule comprisesnucleotides 17521-18975 of SEQ ID NO:7.
 102. The isolated nucleic acidmolecule of claim 87, wherein the nucleic acid molecule consists ofnucleotides 17521-18975 of SEQ ID NO:1.
 103. The isolated nucleic acidmolecule of claim 87, wherein the nucleic acid molecule comprises anucleic acid sequence encoding SEQ ID NO:8.
 104. The isolated nucleicacid molecule of claim 87, wherein the nucleic acid molecule comprisesthe nucleic acid sequence of SEQ ID NO:7.
 105. A recombinant nucleicacid molecule comprising the nucleic acid molecule of claim 87 and atranscription control sequence.
 106. A recombinant plant cell thatexpresses the nucleic acid molecule of claim
 87. 107. A recombinantmicrobial cell that expresses a recombinant vector comprising thenucleic acid molecule of claim 87 and a transcription control sequence.108. The recombinant microbial cell of claim 107, wherein the microbialcell is a bacterium.
 109. The recombinant microbial cell of claim 107,wherein the microbial cell is a Thraustochytriales microorganism. 110.The recombinant microbial cell of claim 109, wherein theThraustochytriales microorganism is a Schizochytrium or aThraustochytrium.
 111. A method to produce at least one polyunsaturatedfatty acid (PUFA), comprising culturing under conditions effective toproduce the PUFA, a plant cell or a microbial cell that expresses a PKSsystem for production of PUFAs, wherein the plant cell or microbial cellexpresses a recombinant vector comprising the nucleic acid molecule ofclaim 87.